AAV4 vector and uses thereof

ABSTRACT

The present invention provides an adeno-associated virus 4 (AAV4) virus and vectors and particles derived therefrom. In addition, the present invention provides methods of delivering a nucleic acid to a cell using the AAV4 vectors and particles.

BACKGROUND OF THE INVENTION

[0001] 1. Field of the Invention

[0002] The present invention provides adeno-associated virus 4 (AAV4) and vectors derived therefrom. Thus, the present invention relates to AAV4 vectors for and methods of delivering nucleic acids to cells of subjects.

[0003] 2. Background Art

[0004] Adeno associated virus (AAV) is a small nonpathogenic virus of the parvoviridae family (for review see 28). AAV is distinct from the other members of this family by its dependence upon a helper virus for replication. In the absence of a helper virus, AAV may integrate in a locus specific manner into the q arm of chromosome 19 (21). The approximately 5 kb genome of AAV consists of one segment of single stranded DNA of either plus or minus polarity. The ends of the genome are short inverted terminal repeats which can fold into hairpin structures and serve as the origin of viral DNA replication. Physically, the parvovirus virion is non-enveloped and its icosahedral capsid is approximately 20 nm in diameter.

[0005] To date 7 serologically distinct AAVs have been identified and 5 have been isolated from humans or primates and are referred to as AAV types 1-5 (1). The most extensively studied of these isolates is AAV type 2 (AAV2). The genome of AAV2 is 4680 nucleotides in length and contains two open reading frames (ORFs). The left ORF encodes the non-structural Rep proteins, Rep40, Rep 52, Rep68 and Rep 78, which are involved in regulation of replication and transcription in addition to the production of single-stranded progeny genomes (5-8, 11, 12, 15, 17, 19, 21-23, 25, 34, 37-40). Furthermore, two of the Rep proteins have been associated with the preferential integration of AAV genomes into a region of the q arm of human chromosome 19. Rep68/78 have also been shown to possess NTP binding activity as well as DNA and RNA helicase activities. The Rep proteins possess a nuclear localization signal as well as several potential phosphorylation sites. Mutation of one of these kinase sites resulted in a loss of replication activity.

[0006] The ends of the genome are short inverted terminal repeats which have the potential to fold into T-shaped hairpin structures that serve as the origin of viral DNA replication. Within the ITR region two elements have been described which are central to the function of the ITR, a GAGC repeat motif and the terminal resolution site (trs). The repeat motif has been shown to bind Rep when the ITR is in either a linear or hairpin conformation (7, 8, 26). This binding serves to position Rep68/78 for cleavage at the trs which occurs in a site- and strand-specific manner. In addition to their role in replication, these two elements appear to be central to viral integration. Contained within the chromosome 19 integration locus is a Rep binding site with an adjacent trs. These elements have been shown to be functional and necessary for locus specific integration.

[0007] The AAV2 virion is a non-enveloped, icosahedral particle approximately 25 nm in diameter, consisting of three related proteins referred to as VP1, 2 and 3. The right ORF encodes the capsid proteins, VP1, VP2, and VP3. These proteins are found in a ratio of 1:1:10 respectively and are all derived from the right-hand ORF. The capsid proteins differ from each other by the use of alternative splicing and an unusual start codon. Deletion analysis has shown that removal or alteration of VP1 which is translated from an alternatively spliced message results in a reduced yield of infections particles (15, 16, 38). Mutations within the VP3 coding region result in the failure to produce any single-stranded progeny DNA or infectious particles (15, 16, 38).

[0008] The following features of AAV have made it an attractive vector for gene transfer (16). AAV vectors have been shown in vitro to stably integrate into the cellular genome; possess a broad host range; transduce both dividing and non dividing cells in vitro and in vivo (13, 20, 30, 32) and maintain high levels of expression of the transduced genes (41). Viral particles are heat stable, resistant to solvents, detergents, changes in pH, temperature, and can be concentrated on CsCl gradients (1,2). Integration of AAV provirus is not associated with any long term negative effects on cell growth or differentiation (3,42). The ITRs have been shown to be the only cis elements required for replication, packaging and integration (35) and may contain some promoter activities (14).

[0009] Initial data indicate that AAV4 is a unique member of this family. DNA hybridization data indicated a similar level of homology for AAV1-4 (31). However, in contrast to the other AAVs only one ORF corresponding to the capsid proteins was identified in AAV4 and no ORF was detected for the Rep proteins (27).

[0010] AAV2 was originally thought to infect a wide variety of cell types provided the appropriate helper virus was present. Recent work has shown that some cell lines are transduced very poorly by AAV2 (30). While the receptor has not been completely characterized, binding studies have indicated that it is poorly expressed on erythroid cells (26). Recombinant AAV2 transduction of CD34⁺, bone marrow pluripotent cells, requires a multiplicity of infection (MOI) of 10⁴ particles per cell (A. W. Nienhuis unpublished results). This suggests that transduction is occurring by a non-specific mechanism or that the density of receptors displayed on the cell surface is low compared to other cell types.

[0011] The present invention provides a vector comprising the AAV4 virus as well as AAV4 viral particles. While AAV4 is similar to AAV2, the two viruses are found herein to be physically and genetically distinct. These differences endow AAV4 with some unique advantages which better suit it as a vector for gene therapy. For example, the wt AAV4 genome is larger than AAV2, allowing for efficient encapsidation of a larger recombinant genome. Furthermore, wt AAV4 particles have a greater buoyant density than AAV2 particles and therefore are more easily separated from contaminating helper virus and empty AAV particles than AAV2-based particles. Additionally, in contrast to AAV1, 2, and 3, AAV4, is able to hemagglutinate human, guinea pig, and sheep erythrocytes (18).

[0012] Furthermore, as shown herein, AAV4 capsid protein, again surprisingly, is distinct from AAV2 capsid protein and exhibits different tissue tropism. AAV2 and AAV4 have been shown to be serologically distinct and thus, in a gene therapy application, AAV4 would allow for transduction of a patient who already possesses neutralizing antibodies to AAV2 either as a result of natural immunological defense or from prior exposure to AAV2 vectors. Thus, the present invention, by providing these new recombinant vectors and particles based on AAV4 provides a new and highly useful series of vectors.

SUMMARY OF THE INVENTION

[0013] The present invention provides a nucleic acid vector comprising a pair of adeno-associated virus 4 (AAV4) inverted terminal repeats and a promoter between the inverted terminal repeats.

[0014] The present invention further provides an AAV4 particle containing a vector comprising a pair of AAV2 inverted terminal repeats.

[0015] Additionally, the instant invention provides an isolated nucleic acid comprising the nucleotide sequence set forth in SEQ ID NO:1 [AAV4 genome]. Furthermore, the present invention provides an isolated nucleic acid consisting essentially of the nucleotide sequence set forth in SEQ ID NO:1 [AAV4 genome].

[0016] The present invention provides an isolated nucleic acid encoding an adeno-associated virus 4 Rep protein. Additionally provided is an isolated AAV4 Rep protein having the amino acid sequence set forth in SEQ ID NO:2, or a unique fragment thereof. Additionally provided is an isolated AAV4 Rep protein having the amino acid sequence set forth in SEQ ID NO:8, or a unique fragment thereof. Additionally provided is an isolated AAV4 Rep protein having the amino acid sequence set forth in SEQ ID NO:9, or a unique fragment thereof. Additionally provided is an isolated AAV4 Rep protein having the amino acid sequence set forth in SEQ ID NO:10, or a unique fragment thereof. Additionally provided is an isolated AAV4 Rep protein having the amino acid sequence set forth in SEQ ID NO:11, or a unique fragment thereof.

[0017] The present invention further provides an isolated AAV4 capsid protein having the amino acid sequence set forth in SEQ ID NO:4. Additionally provided is an isolated AAV4 capsid protein having the amino acid sequence set forth in SEQ ID NO:16. Also provided is an isolated AAV4 capsid protein having the amino acid sequence set forth in SEQ ID NO: 18.

[0018] The present invention additionally provides an isolated nucleic acid encoding adeno-associated virus 4 capsid protein.

[0019] The present invention further provides an AAV4 particle comprising a capsid protein consisting essentially of the amino acid sequence set forth in SEQ ID NO:4.

[0020] Additionally provided by the present invention is an isolated nucleic acid comprising an AAV4 p5 promoter.

[0021] The instant invention provides a method of screening a cell for infectivity by AAV4 comprising contacting the cell with AAV4 and detecting the presence of AAV4 in the cells.

[0022] The present invention further provides a method of delivering a nucleic acid to a cell comprising administering to the cell an AAV4 particle containing a vector comprising the nucleic acid inserted between a pair of AAV inverted terminal repeats, thereby delivering the nucleic acid to the cell.

[0023] The present invention also provides a method of delivering a nucleic acid to a subject comprising administering to a cell from the subject an AAV4 particle comprising the nucleic acid inserted between a pair of AAV inverted terminal repeats, and returning the cell to the subject, thereby delivering the nucleic acid to the subject.

[0024] The present invention further provides a method of delivering a nucleic acid to a subject comprising administering to a cell from the subject an AAV4 particle comprising the nucleic acid inserted between a pair of AAV inverted terminal repeats, and returning the cell to the subject, thereby delivering the nucleic acid to the subject.

[0025] The present invention also provides a method of delivering a nucleic acid to a cell in a subject comprising administering to the subject an AAV4 particle comprising the nucleic acid inserted between a pair of AAV inverted terminal repeats, thereby delivering the nucleic acid to a cell in the subject.

[0026] The instant invention further provides a method of delivering a nucleic acid to a cell in a subject having antibodies to AAV2 comprising administering to the subject an AAV4 particle comprising the nucleic acid, thereby delivering the nucleic acid to a cell in the subject.

BRIEF DESCRIPTION OF THE DRAWINGS

[0027]FIG. 1 shows a schematic outline of AAV 4. Promoters are indicated by horizontal arrows with their corresponding map positions indicated above. The polyadenylation site is indicated by a vertical arrow and the two open reading frames are indicated by black boxes. The splice region is indicated by a shaded box.

[0028]FIG. 2 shows AAV4 ITR. The sequence of the ITR (SEQ ID NO:20) is shown in the hairpin conformation. The putative Rep binding site is boxed. The cleavage site in the trs is indicated by an arrow. Bases which differ from the ITR of AAV2 are outlined.

[0029]FIG. 3 shows cotransduction of rAAV2 and rAAV4. Cos cells were transduced with a constant amount of rAAV2 or rAAV4 expressing beta galactosidase and increasing amounts of rAAV2 expressing human factor IX (rAAV2FIX) . For the competition the number of positive cells detected in the cotransduced wells was divided by the number of positive cells in the control wells (cells transduced with only rAAV2LacZ or rAAV4LacZ) and expressed as a percent of the control. This value was plotted against the number of particles of rAAV2FIX.

[0030]FIG. 4 shows effect of trypsin treatment on cos cell transduction. Cos cell monolayers were trypsinized and diluted in complete media. Cells were incubated with virus at an MOI of 260 and following cell attachment the virus was removed. As a control an equal number of cos cells were plated and allowed to attach overnight before transduction with virus for the same amount of time. The number of positive cells was determined by staining 50 hrs post transduction. The data is presented as a ratio of the number of positive cells seen with the trypsinized group and the control group.

DETAILED DESCRIPTION OF THE INVENTION

[0031] As used in the specification and in the claims, “a” can mean one or more, depending upon the context in which it is used.

[0032] The present invention provides the nucleotide sequence of the adeno-associated virus 4 (AAV4) genome and vectors and particles derived therefrom. Specifically, the present invention provides a nucleic acid vector comprising a pair of AAV4 inverted terminal repeats (ITRs) and a promoter between the inverted terminal repeats. The AAV4 ITRs are exemplified by the nucleotide sequence set forth in SEQ ID NO:6 and SEQ ID NO:20; however, these sequences can have minor modifications and still be contemplated to constitute AAV4 ITRs. The nucleic acid listed in SEQ ID NO:6 depicts the ITR in the “flip” orientation of the ITR. The nucleic acid listed in SEQ ID NO:20 depicts the ITR in the “flop” orientation of the ITR. Minor modifications in an ITR of either orientation are those that will not interfere with the hairpin structure formed by the AAV4 ITR as described herein and known in the art. Furthermore, to be considered within the term “AAV4 ITRs” the nucleotide sequence must retain the Rep binding site described herein and exemplified in SEQ ID NO:6 and SEQ ID NO:20, i.e., it must retain one or both features described herein that distinguish the AAV4 ITR from the AAV2 ITR: (1) four (rather than three as in AAV2) “GAGC” repeats and (2) in the AAV4 ITR Rep binding site the fourth nucleotide in the first two “GAGC” repeats is a T rather than a C.

[0033] The promoter can be any desired promoter, selected by known considerations, such as the level of expression of a nucleic acid functionally linked to the promoter and the cell type in which the vector is to be used. Promoters can be an exogenous or an endogenous promoter. Promoters can include, for example, known strong promoters such as SV40 or the inducible metallothionein promoter, or an AAV promoter, such as an AAV p5 promoter. Additional examples of promoters include promoters derived from actin genes, immunoglobulin genes, cytomegalovirus (CMV), adenovirus, bovine papilloma virus, adenoviral promoters, such as the adenoviral major late promoter, an inducible heat shock promoter, respiratory syncytial virus, Rous sarcomas virus (RSV), etc. Specifically, the promoter can be AAV2 p5 promoter or AAV4 p5 promoter. More specifically, the AAV4 p5 promoter can be about nucleotides 130 to 291 of SEQ ID NO: 1. Additionally, the p5 promoter may be enhanced by nucleotides 1-130. Furthermore, smaller fragments of p5 promoter that retain promoter activity can readily be determined by standard procedures including, for example, constructing a series of deletions in the p5 promoter, linking the deletion to a reporter gene, and determining whether the reporter gene is expressed, i.e., transcribed and/or translated.

[0034] It should be recognized that the nucleotide and amino acid sequences set forth herein may contain minor sequencing errors. Such errors in the nucleotide sequences can be corrected, for example, by using the hybridization procedure described above with various probes derived from the described sequences such that the coding sequence can be reisolated and resequenced. The corresponding amino acid sequence can then be corrected accordingly.

[0035] The AAV4 vector can further comprise an exogenous nucleic acid functionally linked to the promoter. By “heterologous nucleic acid” is meant that any heterologous or exogenous nucleic acid can be inserted into the vector for transfer into a cell, tissue or organism. The nucleic acid can encode a polypeptide or protein or an antisense RNA, for example. By “functionally linked” is meant such that the promoter can promote expression of the heterologous nucleic acid, as is known in the art, such as appropriate orientation of the promoter relative to the heterologous nucleic acid. Furthermore, the heterologous nucleic acid preferably has all appropriate sequences for expression of the nucleic acid, as known in the art, to functionally encode, i.e., allow the nucleic acid to be expressed. The nucleic acid can include, for example, expression control sequences, such as an enhancer, and necessary information processing sites, such as ribosome binding sites, RNA splice sites, polyadenylation sites, and transcriptional terminator sequences.

[0036] The heterologous nucleic acid can encode beneficial proteins that replace missing or defective proteins required by the subject into which the vector in transferred or can encode a cytotoxic polypeptide that can be directed, e.g., to cancer cells or other cells whose death would be beneficial to the subject. The heterologous nucleic acid can also encode antisense RNAs that can bind to, and thereby inactivate, mRNAs made by the subject that encode harmful proteins. In one embodiment, antisense polynucleotides can be produced from a heterologous expression cassette in an AAV4 viral construct where the expression cassette contains a sequence that promotes cell-type specific expression (Wirak et al., EMBO 10:289 (1991)). For general methods relating to antisense polynucleotides, see Antisense RNA and DNA, D. A. Melton, Ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1988).

[0037] Examples of heterologous nucleic acids which can be administered to a cell or subject as part of the present AAV4 vector can include, but are not limited to the following: nucleic acids encoding therapeutic agents, such as tumor necrosis factors (TNF), such as TNF-α; interferons, such as interferon-α, interferon-β, and interferon-γ; interleukins, such as IL-1, IL-1β, and ILs-2 through -14; GM-CSF; adenosine deaminase; cellular growth factors, such as lymphokines; soluble CD4; Factor VIII; Factor IX; T-cell receptors; LDL receptor; ApoE; ApoC; alpha-1 antitrypsin; ornithine transcarbamylase (OTC); cystic fibrosis transmembrane receptor (CFTR); insulin; Fc receptors for antigen binding domains of antibodies, such as immunoglobulins; and antisense sequences which inhibit viral replication, such as antisense sequences which inhibit replication of hepatitis B or hepatitis non-A, non-B virus. The nucleic acid is chosen considering several factors, including the cell to be transfected. Where the target cell is a blood cell, for example, particularly useful nucleic acids to use are those which allow the blood cells to exert a therapeutic effect, such as a gene encoding a clotting factor for use in treatment of hemophilia. Furthermore, the nucleic acid can encode more than one gene product, limited only, if the nucleic acid is to be packaged in a capsid, by the size of nucleic acid that can be packaged.

[0038] Furthermore, suitable nucleic acids can include those that, when transferred into a primary cell, such as a blood cell, cause the transferred cell to target a site in the body where that cell's presence would be beneficial. For example, blood cells such as TIL cells can be modified, such as by transfer into the cell of a Fab portion of a monoclonal antibody, to recognize a selected antigen. Another example would be to introduce a nucleic acid that would target a therapeutic blood cell to tumor cells. Nucleic acids useful in treating cancer cells include those encoding chemotactic factors which cause an inflammatory response at a specific site, thereby having a therapeutic effect.

[0039] Cells, particularly blood cells, having such nucleic acids transferred into them can be useful in a variety of diseases, syndromes and conditions. For example, suitable nucleic acids include nucleic acids encoding soluble CD4, used in the treatment of AIDS and α-antitrypsin, used in the treatment of emphysema caused by α-antitrypsin deficiency. Other diseases, syndromes and conditions in which such cells can be useful include, for example, adenosine deaminase deficiency, sickle cell deficiency, brain disorders such as Alzheimer's disease, thalassemia, hemophilia, diabetes, phenylketonuria, growth disorders and heart diseases, such as those caused by alterations in cholesterol metabolism, and defects of the immune system.

[0040] As another example, hepatocytes can be transfected with the present vectors having useful nucleic acids to treat liver disease. For example, a nucleic acid encoding OTC can be used to transfect hepatocytes (ex vivo and returned to the liver or in vivo) to treat congenital hyperammonemia, caused by an inherited deficiency in OTC. Another example is to use a nucleic acid encoding LDL to target hepatocytes ex vivo or in vivo to treat inherited LDL receptor deficiency. Such transfected hepatocytes can also be used to treat acquired infectious diseases, such as diseases resulting from a viral infection. For example, transduced hepatocyte precursors can be used to treat viral hepatitis, such as hepatitis B and non-A, non-B hepatitis, for example by transducing the hepatocyte precursor with a nucleic acid encoding an antisense RNA that inhibits viral replication. Another example includes transferring a vector of the present invention having a nucleic acid encoding a protein, such as α-interferon, which can confer resistance to the hepatitis virus.

[0041] For a procedure using transfected hepatocytes or hepatocyte precursors, hepatocyte precursors having a vector of the present invention transferred in can be grown in tissue culture, removed form the tissue culture vessel, and introduced to the body, such as by a surgical method. In this example, the tissue would be placed directly into the liver, or into the body cavity in proximity to the liver, as in a transplant or graft. Alternatively, the cells can simply be directly injected into the liver, into the portal circulatory system, or into the spleen, from which the cells can be transported to the liver via the circulatory system. Furthermore, the cells can be attached to a support, such as microcarrier beads, which can then be introduced, such as by injection, into the peritoneal cavity. Once the cells are in the liver, by whatever means, the cells can then express the nucleic acid and/or differentiate into mature hepatocytes which can express the nucleic acid.

[0042] The present invention also contemplates any unique fragment of these AAV4 nucleic acids, including the AAV4 nucleic acids set forth in SEQ ID NOS: 1, 3, 5, 6, 7, 12-15, 17 and 19. To be unique, the fragment must be of sufficient size to distinguish it from other known sequences, most readily determined by comparing any nucleic acid fragment to the nucleotide sequences of nucleic acids in computer databases, such as GenBank. Such comparative searches are standard in the art. Typically, a unique fragment useful as a primer or probe will be at least about 8 or 10 to about 20 or 25 nucleotides in length, depending upon the specific nucleotide content of the sequence. Additionally, fragments can be, for example, at least about 30, 40, 50, 75, 100, 200 or 500 nucleotides in length. The nucleic acid can be single or double stranded, depending upon the purpose for which it is intended.

[0043] The present invention further provides an AAV4 Capsid polypeptide or a unique fragment thereof. AAV4 capsid polypeptide is encoded by ORF 2 of AAV4. Specifically, the present invention provides an AAV4 Capsid protein comprising the amino acid sequence encoded by nucleotides 2260-4467 of the nucleotide sequence set forth in SEQ ID NO:1, or a unique fragment of such protein. The present invention also provides an AAV4 Capsid protein consisting essentially of the amino acid sequence encoded by nucleotides 2260-4467 of the nucleotide sequence set forth in SEQ ID NO:1, or a unique fragment of such protein. The present invention further provides the individual AAV4 coat proteins, VP1, VP2 and VP3. Thus, the present invention provides an isolated polypeptide having the amino acid sequence set forth in SEQ ID NO:4 (VP1). The present invention additionally provides an isolated polypeptide having the amino acid sequence set forth in SEQ ID NO:16 (VP2). The present invention also provides an isolated polypeptide having the amino acid sequence set forth in SEQ ID NO:18 (VP3). By “unique fragment thereof” is meant any smaller polypeptide fragment encoded by any AAV4 capsid gene that is of sufficient length to be unique to the AAV4 Capsid protein. Substitutions and modifications of the amino acid sequence can be made as described above and, further, can include protein processing modifications, such as glycosylation, to the polypeptide. However, an AAV4 Capsid polypeptide including all three coat proteins will have at least about 63% overall homology to the polypeptide encoded by nucleotides 2260-4467 of the sequence set forth in SEQ ID NO:1. The protein can have about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 95% or even 100% homology to the amino acid sequence encoded by the nucleotides 2260-4467 of the sequence set forth in SEQ ID NO:1. An AAV4 VP2 polypeptide can have at least about 58%, about 60%, about 70%, about 80%, about 90% about 95% or about 100% homology to the amino acid sequence set forth in SEQ ID NO:16. An AAV4 VP3 polypeptide can have at least about 60%, about 70%, about 80%, about 90% about 95% or about 100% homology to the amino acid sequence set forth in SEQ ID NO:18.

[0044] The herein described AAV4 nucleic acid vector can be encapsidated in an AAV particle. In particular, it can be encapsidated in an AAV1 particle, an AAV2 particle, an AAV3 particle, an AAV4 particle, or an AAV5 particle by standard methods using the appropriate capsid proteins in the encapsidation process, as long as the nucleic acid vector fits within the size limitation of the particle utilized. The encapsidation process itself is standard in the art.

[0045] An AAV4 particle is a viral particle comprising an AAV4 capsid protein. An AAV4 capsid polypeptide encoding the entire VP1, VP2, and VP3 polypeptide can overall have at least about 63% homology to the polypeptide having the amino acid sequence encoded by nucleotides 2260-4467 set forth in SEQ ID NO:1 (AAV4 capsid protein). The capsid protein can have about 70% homology, about 75% homology, 80% homology, 85% homology, 90% homology, 95% homology, 98% homology, 99% homology, or even 100% homology to the protein having the amino acid sequence encoded by nucleotides 2260-4467 set forth in SEQ ID NO:1. The particle can be a particle comprising both AAV4 and AAV2 capsid protein, i.e., a chimeric protein. Variations in the amino acid sequence of the AAV4 capsid protein are contemplated herein, as long as the resulting viral particle comprising the AAV4 capsid remains antigenically or immunologically distinct from AAV2, as can be routinely determined by standard methods. Specifically, for example, ELISA and Western blots can be used to determine whether a viral particle is antigenically or immunologically distinct from AAV2. Furthermore, the AAV4 viral particle preferably retains tissue tropism distinction from AAV2, such as that exemplified in the examples herein, though an AAV4 chimeric particle comprising at least one AAV4 coat protein may have a different tissue tropism from that of an AAV4 particle consisting only of AAV4 coat proteins.

[0046] An AAV4 particle is a viral particle comprising an AAV4 capsid protein. An AAV4 capsid polypeptide encoding the entire VP1, VP2, and VP3 polypeptide can overall have at least about 63% homology to the polypeptide having the amino acid sequence encoded by nucleotides 2260-4467 set forth in SEQ ID NO:1 (AAV4 capsid protein). The capsid protein can have about 70% homology, about 75% homology, 80% homology, 85% homology, 90% homology, 95% homology, 98% homology, 99% homology, or even 100% homology to the protein having the amino acid sequence encoded by nucleotides 2260-4467 set forth in SEQ ID NO:1. The particle can be a particle comprising both AAV4 and AAV2 capsid protein, i.e., a chimeric protein. Variations in the amino acid sequence of the AAV4 capsid protein are contemplated herein, as long as the resulting viral particle comprising the AAV4 capsid remains antigenically or immunologically distinct from AAV2, as can be routinely determined by standard methods. Specifically, for example, ELISA and Western blots can be used to determine whether a viral particle is antigenically or immunologically distinct from AAV2. Furthermore, the AAV4 viral particle preferably retains tissue tropism distinction from AAV2, such as that exemplified in the examples herein, though an AAV4 chimeric particle comprising at least one AAV4 coat protein may have a different tissue tropism from that of an AAV4 particle consisting only of AAV4 coat proteins.

[0047] The invention further provides an AAV4 particle containing, i.e., encapsidating, a vector comprising a pair of AAV2 inverted terminal repeats. The nucleotide sequence of AAV2 ITRs is known in the art. Furthermore, the particle can be a particle comprising both AAV4 and AAV2 capsid protein, i.e., a chimeric protein. The vector encapsidated in the particle can further comprise an exogenous nucleic acid inserted between the inverted terminal repeats.

[0048] The present invention further provides an isolated nucleic acid comprising the nucleotide sequence set forth in SEQ ID NO:1 (AAV4 genome). This nucleic acid, or portions thereof, can be inserted into other vectors, such as plasmids, yeast artificial chromosomes, or other viral vectors, if desired, by standard cloning methods. The present invention also provides an isolated nucleic acid consisting essentially of the nucleotide sequence set forth in SEQ ID NO:1. The nucleotides of SEQ ID NO:1 can have minor modifications and still be contemplated by the present invention. For example, modifications that do not alter the amino acid encoded by any given codon (such as by modification of the third, “wobble,” position in a codon) can readily be made, and such alterations are known in the art. Furthermore, modifications that cause a resulting neutral amino acid substitution of a similar amino acid can be made in a coding region of the genome. Additionally, modifications as described herein for the AAV4 components, such as the ITRs, the p5 promoter, etc. are contemplated in this invention.

[0049] The present invention additionally provides an isolated nucleic acid that selectively hybridizes with an isolated nucleic acid consisting essentially of the nucleotide sequence set forth in SEQ ID NO:1 (AAV4 genome). The present invention further provides an isolated nucleic acid that selectively hybridizes with an isolated nucleic acid comprising the nucleotide sequence set forth in SEQ ID NO:1 (AAV4 genome). By “selectively hybridizes” as used in the claims is meant a nucleic acid that specifically hybridizes to the particular target nucleic acid under sufficient stringency conditions to selectively hybridize to the target nucleic acid without significant background hybridization to a nucleic acid encoding an unrelated protein, and particularly, without detectably hybridizing to AAV2. Thus, a nucleic acid that selectively hybridizes with a nucleic acid of the present invention will not selectively hybridize under stringent conditions with a nucleic acid encoding a different protein, and vice versa. Therefore, nucleic acids for use, for example, as primers and probes to detect or amplify the target nucleic acids are contemplated herein. Nucleic acid fragments that selectively hybridize to any given nucleic acid can be used, e.g., as primers and or probes for further hybridization or for amplification methods (e.g., polymerase chain reaction (PCR), ligase chain reaction (LCR)). Additionally, for example, a primer or probe can be designed that selectively hybridizes with both AAV4 and a gene of interest carried within the AAV4 vector (i.e., a chimeric nucleic acid).

[0050] Stringency of hybridization is controlled by both temperature and salt concentration of either or both of the hybridization and washing steps. Typically, the stringency of hybridization to achieve selective hybridization involves hybridization in high ionic strength solution (6× SSC or 6× SSPE) at a temperature that is about 12-25° C. below the T_(m) (the melting temperature at which half of the molecules dissociate from its partner) followed by washing at a combination of temperature and salt concentration chosen so that the washing temperature is about 5° C. to 20° C. below the T_(m) The temperature and salt conditions are readily determined empirically in preliminary experiments in which samples of reference DNA immobilized on filters are hybridized to a labeled nucleic acid of interest and then washed under conditions of different stringencies. Hybridization temperatures are typically higher for DNA-RNA and RNA-RNA hybridizations. The washing temperatures can be used as described above to achieve selective stringency, as is known in the art. (Sambrook et al., Molecular Cloning: A Laboratory Manual, 2nd Ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 1989; Kunkel et al. Methods Enzymol. 1987:154:367, 1987). A preferable stringent hybridization condition for a DNA:DNA hybridization can be at about 68° C. (in aqueous solution) in 6× SSC or 6× SSPE followed by washing at 68° C. Stringency of hybridization and washing, if desired, can be reduced accordingly as homology desired is decreased, and further, depending upon the G-C or A-T richness of any area; wherein variability is searched for. Likewise, stringency of hybridization and washing, if desired, can be increased accordingly as homology desired is increased, and further, depending upon the G-C or A-T richness of any area wherein high homology is desired, all as known in the art.

[0051] A nucleic acid that selectively hybridizes to any portion of the AAV4 genome is contemplated herein. Therefore, a nucleic acid that selectively hybridizes to AAV4 can be of longer length than the AAV4 genome, it can be about the same length as the AAV4 genome or it can be shorter than the AAV4 genome. The length of the nucleic acid is limited on the shorter end of the size range only by its specificity for hybridization to AAV4, i.e., once it is too short, typically less than about 5 to 7 nucleotides in length, it will no longer bind specifically to AAV4, but rather will hybridize to numerous background nucleic acids. Additionally contemplated by this invention is a nucleic acid that has a portion that specifically hybridizes to AAV4 and a portion that specifically hybridizes to a gene of interest inserted within AAV4.

[0052] The present invention further provides an isolated nucleic acid encoding an adeno-associated virus 4 Rep protein. The AAV4 Rep proteins are encoded by open reading frame (ORF) 1 of the AAV4 genome. The AAV4 Rep genes are exemplified by the nucleic acid set forth in SEQ ID NO:3 (AAV4 ORF1), and include a nucleic acid consisting essentially of the nucleotide sequence set forth in SEQ ID NO:3 and a nucleic acid comprising the nucleotide sequence set forth in SEQ ID NO:3. The present invention also includes a nucleic acid encoding the amino acid sequence set forth in SEQ ID NO: 2 (polypeptide encoded by AAV4 ORF1). However, the present invention includes that the Rep genes nucleic acid can include any one, two, three, or four of the four Rep proteins, in any order, in such a nucleic acid. Furthermore, minor modifications are contemplated in the nucleic acid, such as silent mutations in the coding sequences, mutations that make neutral or conservative changes in the encoded amino acid sequence, and mutations in regulatory regions that do not disrupt the expression of the gene. Examples of other minor modifications are known in the art. Further modifications can be made in the nucleic acid, such as to disrupt or alter expression of one or more of the Rep proteins in order to, for example, determine the effect of such a disruption; such as to mutate one or more of the Rep proteins to determine the resulting effect, etc. However, in general, a modified nucleic acid encoding all four Rep proteins will have at least about 90%, about 93%, about 95%, about 98% or 100% homology to the sequence set forth in SEQ ID NO:3, and the Rep polypeptide encoded therein will have overall about 93%, about 95%, about 98%, about 99% or 100% homology with the amino acid sequence set forth in SEQ ID NO:2.

[0053] The present invention also provides an isolated nucleic acid that selectively hybridizes with a nucleic acid consisting essentially of the nucleotide sequence set forth in SEQ ID NO:3 and an isolated nucleic acid that selectively hybridizes with a nucleic acid comprising the nucleotide sequence set forth in SEQ ID NO:3. “Selectively hybridizing” is defined elsewhere herein.

[0054] The present invention also provides each individual AAV4 Rep protein and the nucleic acid encoding each. Thus the present invention provides the nucleic acid encoding a Rep 40 protein, and in particular an isolated nucleic acid comprising the nucleotide sequence set forth in SEQ ID NO:12, an isolated nucleic acid consisting essentially of the nucleotide sequence set forth in SEQ ID NO:12, and a nucleic acid encoding the adeno-associated virus 4 Rep protein having the amino acid sequence set forth in SEQ ID NO:8. The present invention also provides the nucleic acid encoding a Rep 52 protein, and in particular an isolated nucleic acid comprising the nucleotide sequence set forth in SEQ ID NO:13, an isolated nucleic acid consisting essentially of the nucleotide sequence set forth in SEQ ID NO:13, and a nucleic acid encoding the adeno-associated virus 4 Rep protein having the amino acid sequence set forth in SEQ ID NO:9. The present invention further provides the nucleic acid encoding a Rep 68 protein, and in particular an isolated nucleic acid comprising the nucleotide sequence set forth in SEQ ID NO:14, an isolated nucleic acid consisting essentially of the nucleotide sequence set forth in SEQ ID NO:14, and a nucleic acid encoding the adeno-associated virus 4 Rep protein having the amino acid sequence set forth in SEQ ID NO:10. And, further, the present invention provides the nucleic acid encoding a Rep 78 protein, and in particular an isolated nucleic acid comprising the nucleotide sequence set forth in SEQ ID NO:15, an isolated nucleic acid consisting essentially of the nucleotide sequence set forth in SEQ ID NO:15, and a nucleic acid encoding the adeno-associated virus 4 Rep protein having the amino acid sequence set forth in SEQ ID NO:11. As described elsewhere herein, these nucleic acids can have minor modifications, including silent nucleotide substitutions, mutations causing neutral amino acid substitutions in the encoded proteins, and mutations in control regions that do not or minimally affect the encoded amino acid sequence.

[0055] The present invention further provides a nucleic acid encoding the entire AAV4 Capsid polypeptide. Specifically, the present invention provides a nucleic acid having the nucleotide sequence set for the nucleotides 2260-4467 of SEQ ID NO:1. Furthermore, the present invention provides a nucleic acid encoding each of the three AAV4 coat proteins, VP1, VP2, and VP3. Thus, the present invention provides a nucleic acid encoding AAV4 VP1, a nucleic acid encoding AAV4 VP2, and a nucleic acid encoding AAV4 VP3. Thus, the present invention provides a nucleic acid encoding the amino acid sequence set forth in SEQ ID NO:4 (VP1); a nucleic acid encoding the amino acid sequence set forth in SEQ ID NO:16 (VP2), and a nucleic acid encoding the amino acid sequence set forth in SEQ ID NO:18 (VP3). The present invention also specifically provides a nucleic acid comprising SEQ ID NO:5 (VP1 gene); a nucleic acid comprising SEQ ID NO:17 (VP2 gene); and a nucleic acid comprising SEQ ID NO:19 (VP3 gene). The present invention also specifically provides a nucleic acid consisting essentially of SEQ ID NO:5 (VP1 gene), a nucleic acid consisting essentially of SEQ ID NO:17 (VP2 gene), and a nucleic acid consisting essentially of SEQ ID NO:19 (VP3 gene). Furthermore, a nucleic acid encoding an AAV4 capsid protein VP1 is set forth as nucleotides 2260-4467 of SEQ ID NO:1; a nucleic acid encoding an AAV4 capsid protein VP2 is set forth as nucleotides 2668-4467 of SEQ ID NO:1; and a nucleic acid encoding an AAV4 capsid protein VP3 is set forth as nucleotides 2848-4467 of SEQ ID NO:1. Minor modifications in the nucleotide sequences encoding the capsid, or coat, proteins are contemplated, as described above for other AAV4 nucleic acids.

[0056] The present invention also provides a cell containing one or more of the herein described nucleic acids, such as the AAV4 genome, AAV4 ORF1 and ORF2, each AAV4 Rep protein gene, and each AAV4 capsid protein gene. Such a cell can be any desired cell and can be selected based upon the use intended. For example, cells can include human HeLa cells, cos cells, other human and mammalian cells and cell lines. Primary cultures as well as established cultures and cell lines can be used. Nucleic acids of the present invention can be delivered into cells by any selected means, in particular depending upon the target cells. Many delivery means are well-known in the art. For example, electroporation, calcium phosphate precipitation, microinjection, cationic or anionic liposomes, and liposomes in combination with a nuclear localization signal peptide for delivery to the nucleus can be utilized, as is known in the art. Additionally, if in a viral particle, the cells can simply be transfected with the particle by standard means known in the art for AAV transfection.

[0057] The term “polypeptide” as used herein refers to a polymer of amino acids and includes full-length proteins and fragments thereof. Thus, “protein,” polypeptide,” and “peptide” are often used interchangeably herein. Substitutions can be selected by known parameters to be neutral (see, e.g., Robinson W E Jr., and Mitchell W M., AIDS 4:S151-S162 (1990)). As will be appreciated by those skilled in the art, the invention also includes those polypeptides having slight variations in amino acid sequences or other properties. Such variations may arise naturally as allelic variations (e.g., due to genetic polymorphism) or may be produced by human intervention (e.g., by mutagenesis of cloned DNA sequences), such as induced point, deletion, insertion and substitution mutants. Minor changes in amino acid sequence are generally preferred, such as conservative amino acid replacements, small internal deletions or insertions, and additions or deletions at the ends of the molecules. Substitutions may be designed based on, for example, the model of Dayhoff, et al. (in Atlas of Protein Sequence and Structure 1978, Nat'l Biomed. Res. Found., Washington, D.C.). These modifications can result in changes in the amino acid sequence, provide silent mutations, modify a restriction site, or provide other specific mutations.

[0058] A polypeptide of the present invention can be readily obtained by any of several means. For example, polypeptide of interest can be synthesized mechanically by standard methods. Additionally, the coding regions of the genes can be expressed and the resulting polypeptide isolated by standard methods. Furthermore, an antibody specific for the resulting polypeptide can be raised by standard methods (see, e.g., Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 1988), and the protein can be isolated from a cell expressing the nucleic acid encoding the polypeptide by selective hybridization with the antibody. This protein can be purified to the extent desired by standard methods of protein purification (see, e.g., Sambrook et al., Molecular Cloning: A Laboratory Manual, 2nd Ed., Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 1989).

[0059] Typically, to be unique, a polypeptide fragment of the present invention will be at least about 5 amino acids in length; however, unique fragments can be 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100 or more amino acids in length. A unique polypeptide will typically comprise such a unique fragment; however, a unique polypeptide can also be determined by its overall homology. A unique polypeptide can be 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100 or more amino acids in length. Uniqueness of a polypeptide fragment can readily be determined by standard methods such as searches of computer databases of known peptide or nucleic acid sequences or by hybridization studies to the nucleic acid encoding the protein or to the protein itself, as known in the art.

[0060] The present invention provides an isolated AAV4 Rep protein. AAV4 Rep polypeptide is encoded by ORF1 of AAV4. Specifically, the present invention provides an AAV4 Rep polypeptide comprising the amino acid sequence set forth in SEQ ID NO:2, or a unique fragment thereof. The present invention also provides an AAV4 Rep polypeptide consisting essentially of the amino acid sequence set forth in SEQ ID NO:2, or a unique fragment thereof. Additionally, nucleotides 291-2306 of the AAV4 genome, which genome is set forth in SEQ ID NO:1, encode the AAV4 Rep polypeptide. The present invention also provides each AAV4 Rep protein. Thus the present invention provides AAV4 Rep 40, or a unique fragment thereof. The present invention particularly provides Rep 40 having the amino acid sequence set forth in SEQ ID NO:8. The present invention provides AAV4 Rep 52, or a unique fragment thereof. The present invention particularly provides Rep 52 having the amino acid sequence set forth in SEQ ID NO:9. The present invention provides AAV4 Rep 68, or a unique fragment thereof. The present invention particularly provides Rep 68 having the amino acid sequence set forth in SEQ ID NO:10. The present invention provides AAV4 Rep 78, or a unique fragment thereof. The present invention particularly provides Rep 78 having the amino acid sequence set forth in SEQ ID NO:11. By “unique fragment thereof” is meant any smaller polypeptide fragment encoded by AAV rep gene that is of sufficient length to be unique to the Rep polypeptide. Substitutions and modifications of the amino acid sequence can be made as described above and, further, can include protein processing modifications, such as glycosylation, to the polypeptide. However, a polypeptide including all four Rep proteins will encode a polypeptide having at least about 91% overall homology to the sequence set forth in SEQ ID NO:2, and it can have about 93%, about 95%, about 98%, about 99% or 100% homology with the amino acid sequence set forth in SEQ ID NO:2.

[0061] The present invention further provides an AAV4 Capsid polypeptide or a unique fragment thereof. AAV4 capsid polypeptide is encoded by ORF 2 of AAV4. Specifically, the present invention provides an AAV4 Capsid protein comprising the amino acid sequence encoded by nucleotides 2260-4467of the nucleotide sequence set forth in SEQ ID NO:1, or a unique fragment of such protein. The present invention also provides an AAV4 Capsid protein consisting essentially of the amino acid sequence encoded by nucleotides 2260-4467 of the nucleotide sequence set forth in SEQ ID NO:1, or a unique fragment of such protein. The present invention further provides the individual AAV4 coat proteins, VP1, VP2 and VP3. Thus, the present invention provides an isolated polypeptide having the amino acid sequence set forth in SEQ ID NO:4 (VP 1). The present invention additionally provides an isolated polypeptide having the amino acid sequence set forth in SEQ ID NO:16 (VP2). The present invention also provides an isolated polypeptide having the amino acid sequence set forth in SEQ ID NO:18 (VP3). By “unique fragment thereof” is meant any smaller polypeptide fragment encoded by any AAV4 capsid gene that is of sufficient length to be unique to the AAV4 Capsid protein. Substitutions and modifications of the amino acid sequence can be made as described above and, further, can include protein processing modifications, such as glycosylation, to the polypeptide. However, an AAV4 Capsid polypeptide including all three coat proteins will have at least about 63% overall homology to the polypeptide encoded by nucleotides 2260-4467 of the sequence set forth in SEQ ID NO:1. The protein can have about 65%, about 70%, about 75%, about 80%, about 85%, about 90%, about 95% or even 100% homology to the amino acid sequence encoded by the nucleotides 2260-4467 of the sequence set forth in SEQ ID NO:4. An AAV4 VP2 polypeptide can have at least about 58%, about 60%, about 70%, about 80%, about 90% about 95% or about 100% homology to the amino acid sequence set forth in SEQ ID NO:16. An AAV4 VP3 polypeptide can have at least about 60%, about 70%, about 80%, about 90% about 95% or about 100% homology to the amino acid sequence set forth in SEQ ID NO:18.

[0062] The present invention further provides an isolated antibody that specifically binds AAV4 Rep protein. Also provided is an isolated antibody that specifically binds the AAV4 Rep protein having the amino acid sequence set forth in SEQ ID NO:2, or that specifically binds a unique fragment thereof. Clearly, any given antibody can recognize and bind one of a number of possible epitopes present in the polypeptide; thus only a unique portion of a polypeptide (having the epitope) may need to be present in an assay to determine if the antibody specifically binds the polypeptide.

[0063] The present invention additionally provides an isolated antibody that specifically binds any adeno-associated virus 4 Capsid protein or the polypeptide comprising all three AAV4 coat proteins. Also provided is an isolated antibody that specifically binds the AAV4 Capsid protein having the amino acid sequence set forth in SEQ ID NO:4, or that specifically binds a unique fragment thereof. The present invention further provides an isolated antibody that specifically binds the AAV4 Capsid protein having the amino acid sequence set forth in SEQ ID NO:16, or that specifically binds a unique fragment thereof. The invention additionally provides an isolated antibody that specifically binds the AAV4 Capsid protein having the amino acid sequence set forth in SEQ ID NO:18, or that specifically binds a unique fragment thereof. Again, any given antibody can recognize and bind one of a number of possible epitopes present in the polypeptide; thus only a unique portion of a polypeptide (having the epitope) may need to be present in an assay to determine if the antibody specifically binds the polypeptide.

[0064] The antibody can be a component of a composition that comprises an antibody that specifically binds the AAV4 protein. The composition can further comprise, e.g., serum, serum-free medium, or a pharmaceutically acceptable carrier such as physiological saline, etc.

[0065] By “an antibody that specifically binds” an AAV4 polypeptide or protein is meant an antibody that selectively binds to an epitope on any portion of the AAV4 peptide such that the antibody selectively binds to the AAV4 polypeptide, i.e., such that the antibody binds specifically to the corresponding AAV4 polypeptide without significant background. Specific binding by an antibody further means that the antibody can be used to selectively remove the target polypeptide from a sample comprising the polypeptide or and can readily be determined by radioimmunoassay (RIA), bioassay, or enzyme-linked immunosorbant (ELISA) technology. An ELISA method effective for the detection of the specific antibody-antigen binding can, for example, be as follows: (1) bind the antibody to a substrate; (2) contact the bound antibody with a sample containing the antigen; (3) contact the above with a secondary antibody bound to a detectable moiety (e.g., horseradish peroxidase enzyme or alkaline phosphatase enzyme); (4) contact the above with the substrate for the enzyme; (5) contact the above with a color reagent; (6) observe the color change.

[0066] An antibody can include antibody fragments such as Fab fragments which retain the binding activity. Antibodies can be made as described in, e.g., Harlow and Lane, Antibodies: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1988). Briefly, purified antigen can be injected into an animal in an amount and in intervals sufficient to elicit an immune response. Antibodies can either be purified directly, or spleen cells can be obtained from the animal. The cells are then fused with an immortal cell line and screened for antibody secretion. Individual hybridomas are then propagated as individual clones serving as a source for a particular monoclonal antibody.

[0067] The present invention additionally provides a method of screening a cell for infectivity by AAV4 comprising contacting the cell with AAV4 and detecting the presence of AAV4 in the cells. AAV4 particles can be detected using any standard physical or biochemical methods. For example, physical methods that can be used for this detection include 1) polymerase chain reaction (PCR) for viral DNA or RNA, 2) direct hybridization with labeled probes, 3) antibody directed against the viral structural or non-structural proteins. Catalytic methods of viral detection include, but are not limited to, detection of site and strand specific DNA nicking activity of Rep proteins or replication of an AAV origin-containing substrate. Additional detection methods are outlined in Fields, Virology, Raven Press, New York, N.Y. 1996.

[0068] For screening a cell for infectivity by AAV4 wherein the presence of AAV4 in the cells is determined by nucleic acid hybridization methods, a nucleic acid probe for such detection can comprise, for example, a unique fragment of any of the AAV4 nucleic acids provided herein. The uniqueness of any nucleic acid probe can readily be determined as described herein for unique nucleic acids. The nucleic acid can be, for example, the nucleic acid whose nucleotide sequence is set forth in SEQ ID NO: 1, 3, 5, 6, 7, 12, 13, 14, 15, 17 or 19, or a unique fragment thereof.

[0069] The present invention includes a method of determining the suitability of an AAV4 vector for administration to a subject comprising administering to an antibody-containing sample from the subject an antigenic fragment of an isolated AAV4 capsid protein, and detecting an antibody-antigen reaction in the sample, the presence of a reaction indicating the AAV4 vector to be unsuitable for use in the subject. The AAV4 capsid protein from which an antigenic fragment is selected can have the amino acid sequence set forth in SEQ ID NO:4. An immunogenic fragment of an isolated AAV4 capsid protein can also be used in these methods. The AAV4 capsid protein from which an antigenic fragment is selected can have the amino acid sequence set forth in SEQ ID NO:17. The AAV4 capsid protein from which an antigenic fragment is selected can have the amino acid sequence set forth in SEQ ID NO:19.

[0070] Alternatively, or additionally, an antigenic fragment of an isolated AAV4 Rep protein can be utilized in this determination method. An immunogenic fragment of an isolated AAV4 Rep protein can also be used in these methods. Thus the present invention further provides a method of determining the suitability of an AAV4 vector for administration to a subject comprising administering to an antibody-containing sample from the subject an antigenic fragment of an AAV4 Rep protein and detecting an antibody-antigen reaction in the sample, the presence of a reaction indicating the AAV4 vector to be unsuitable for use in the subject. The AAV4 Rep protein from which an antigenic fragment is selected can have the amino acid sequence set forth in SEQ ID NO:2. The AAV4 Rep protein from which an antigenic fragment is selected can have the amino acid sequence set forth in SEQ ID NO:8. The AAV4 Rep protein from which an antigenic fragment is selected can have the amino acid sequence set forth in SEQ ID NO:9. The AAV4 Rep protein from which an antigenic fragment is selected can have the amino acid sequence set forth in SEQ ID NO:10. The AAV4 Rep protein from which an antigenic fragment is selected can have the amino acid sequence set forth in SEQ ID NO:11.

[0071] An antigenic or immunoreactive fragment is typically an amino acid sequence of at least about 5 consecutive amino acids, and it can be derived from the AAV4 polypeptide amino acid sequence. An antigenic fragment is any fragment unique to the AAV4 protein, as described herein, against which an AAV4-specific antibody can be raised, by standard methods. Thus, the resulting antibody-antigen reaction should be specific for AAV4.

[0072] The AAV4 polypeptide fragments can be analyzed to determine their antigenicity, immunogenicity and/or specificity. Briefly, various concentrations of a putative immunogenically specific fragment are prepared and administered to a subject and the immunological response (e.g., the production of antibodies or cell mediated immunity) of an animal to each concentration is determined. The amounts of antigen administered depend on the subject, e.g. a human, rabbit or a guinea pig, the condition of the subject, the size of the subject, etc. Thereafter an animal so inoculated with the antigen can be exposed to the AAV4 viral particle or AAV4 protein to test the immunoreactivity or the antigenicity of the specific immunogenic fragment. The specificity of a putative antigenic or immunogenic fragment can be ascertained by testing sera, other fluids or lymphocytes from the inoculated animal for cross reactivity with other closely related viruses, such as AAV1, AAV2, AAV3 and AAV5.

[0073] As will be recognized by those skilled in the art, numerous types of immunoassays are available for use in the present invention to detect binding between an antibody and an AAV4 polypeptide of this invention. For instance, direct and indirect binding assays, competitive assays, sandwich assays, and the like, as are generally described in, e.g., U.S. Pat. Nos. 4,642,285; 4,376,110; 4,016,043; 3,879,262; 3,852,157; 3,850,752; 3,839,153; 3,791,932; and Harlow and Lane, Antibodies, A Laboratory Manual, Cold Spring Harbor Publications, N.Y. (1988). For example, enzyme immunoassays such as immunofluorescence assays. (IFA), enzyme linked immunosorbent assays (ELISA) and immunoblotting can be readily adapted to accomplish the detection of the antibody. An ELISA method effective for the detection of the antibody bound to the antigen can, for example, be as follows: (1) bind the antigen to a substrate; (2) contact the bound antigen with a fluid or tissue sample containing the antibody; (3) contact the above with a secondary antibody specific for the antigen and bound to a detectable moiety (e.g., horseradish peroxidase enzyme or alkaline phosphatase enzyme); (4) contact the above with the substrate for the enzyme; (5) contact the above with a color reagent; (6) observe color change.

[0074] The antibody-containing sample of this method can comprise any biological sample which would contain the antibody or a cell containing the antibody, such as blood, plasma, serum, bone marrow, saliva and urine.

[0075] By the “suitability of an AAV4 vector for administration to a subject” is meant a determination of whether the AAV4 vector will elicit a neutralizing immune response upon administration to a particular subject. A vector that does not elicit a significant immune response is a potentially suitable vector, whereas a vector that elicits a significant, neutralizing immune response is thus indicated to be unsuitable for use in that subject. Significance of any detectable immune response is a standard parameter understood by the skilled artisan in the field. For example, one can incubate the subject's serum with the virus, then determine whether that virus retains its ability to transduce cells in culture. If such virus cannot transduce cells in culture, the vector likely has elicited a significant immune response.

[0076] The present method further provides a method of delivering a nucleic acid to a cell comprising administering to the cell an AAV4 particle containing a vector comprising the nucleic acid inserted between a pair of AAV inverted terminal repeats, thereby delivering the nucleic acid to the cell. Administration to the cell can be accomplished by any means, including simply contacting the particle, optionally contained in a desired liquid such as tissue culture medium, or a buffered saline solution, with the cells. The particle can be allowed to remain in contact with the cells for any desired length of time, and typically the particle is administered and allowed to remain indefinitely. For such in vitro methods, the virus can be administered to the cell by standard viral transduction methods, as known in the art and as exemplified herein. Titers of virus to administer can vary, particularly depending upon the cell type, but will be typical of that used for AAV transduction in general. Additionally the titers used to transduce the particular cells in the present examples can be utilized. The cells can include any desired cell, such as the following cells and cells derived from the following tissues, in humans as well as other mammals, such as primates, horse, sheep, goat, pig, dog, rat, and mouse: Adipocytes, Adenocyte, Adrenal cortex, Amnion, Aorta, Ascites, Astrocyte, Bladder, Bone, Bone marrow, Brain, Breast, Bronchus, Cardiac muscle, Cecum, Cervix, Chorion, Colon, Conjunctiva, Connective tissue, Cornea, Dermis, Duodenum, Endometrium, Endothelium, Epithelial tissue, Epidermis, Esophagus, Eye, Fascia, Fibroblasts, Foreskin, Gastric, Glial cells, Glioblast, Gonad, Hepatic cells, Histocyte, Ileum, Intestine, small Intestine, Jejunum, Keratinocytes, Kidney, Larynx, Leukocytes, Lipocyte, Liver, Lung, Lymph node, Lymphoblast, Lymphocytes, Macrophages, Mammary alveolar nodule, Mammary gland, Mastocyte, Maxilla, Melanocytes, Monocytes, Mouth, Myelin, Nervous tissue, Neuroblast, Neurons, Neuroglia, Osteoblasts, Osteogenic cells, Ovary, Palate, Pancreas, Papilloma, Peritoneum, Pituicytes, Pharynx, Placenta, Plasma cells, Pleura, Prostate, Rectum, Salivary gland, Skeletal muscle, Skin, Smooth muscle, Somatic, Spleen, Squamous, Stomach, Submandibular gland, Submaxillary gland, Synoviocytes, Testis, Thymus, Thyroid, Trabeculae, Trachea, Turbinate, Umbilical cord, Ureter, and Uterus.

[0077] The AAV inverted terminal repeats in the vector for the herein described delivery methods can be AAV4 inverted terminal repeats. Specifically, they can comprise the nucleic acid whose nucleotide sequence is set forth in SEQ ID NO:6 or the nucleic acid whose nucleotide sequence is set forth in SEQ ID NO:20, or any fragment thereof demonstrated to have ITR functioning. The ITRs can also consist essentially of the nucleic acid whose nucleotide sequence is set forth in SEQ ID NO:6 or the nucleic acid whose nucleotide sequence is set forth in SEQ ID NO:20. Furthermore, the AAV inverted terminal repeats in the vector for the herein described nucleic acid delivery methods can also comprise AAV2 inverted terminal repeats. Additionally, the AAV inverted terminal repeats in the vector for this delivery method can also consist essentially of AAV2 inverted terminal repeats.

[0078] The present invention also includes a method of delivering a nucleic acid to a subject comprising administering to a cell from the subject an AAV4 particle comprising the nucleic acid inserted between a pair of AAV inverted terminal repeats, and returning the cell to the subject, thereby delivering the nucleic acid to the subject. The AAV ITRs can be any, AAV ITRs, including AAV4 ITRs and AAV2 ITRs. For such an ex vivo administration, cells are isolated from a subject by standard means according to the cell type and placed in appropriate culture medium, again according to cell type (see, e.g., ATCC catalog). Viral particles are then contacted with the cells as described above, and the virus is allowed to transfect the cells. Cells can then be transplanted back into the subject's body, again by means standard for the cell type and tissue (e. g., in general, U.S. Pat. No. 5,399,346; for neural cells, Dunnett, S. B. and Björklund, A., eds., Transplantation: Neural Transplantation—A Practical Approach, Oxford University Press, Oxford (1992)). If desired, prior to transplantation, the cells can be studied for degree of transfection by the virus, by known detection means and as described herein. Cells for ex vivo transfection followed by transplantation into a subject can be selected from those listed above, or can be any other selected cell. Preferably, a selected cell type is examined for its capability to be transfected by AAV4. Preferably, the selected cell will be a cell readily transduced with AAV4 particles; however, depending upon the application, even cells with relatively low transduction efficiencies can be useful, particularly if the cell is from a tissue or organ in which even production of a small amount of the protein or antisense RNA encoded by the vector will be beneficial to the subject.

[0079] The present invention further provides a method of delivering a nucleic acid to a cell in a subject comprising administering to the subject an AAV4 particle comprising the nucleic acid inserted between a pair of AAV inverted terminal repeats, thereby delivering the nucleic acid to a cell in the subject. Administration can be an ex vivo administration directly to a cell removed from a subject, such as any of the cells listed above, followed by replacement of the cell back into the subject, or administration can be in vivo administration to a cell in the subject. For ex vivo administration, cells are isolated from a subject by standard means according to the cell type and placed in appropriate culture medium, again according to cell type (see, e.g., ATCC catalog). Viral particles are then contacted with the cells as described above, and the virus is allowed to transfect the cells. Cells can then be transplanted back into the subject's body, again by means standard for the cell type and tissue (e. g., for neural cells, Dunnett, S. B. and Björklund, A., eds., Transplantation: Neural Transplantation—A Practical Approach, Oxford University Press, Oxford (1992)). If desired, prior to transplantation, the cells can be studied for degree of transfection by the virus, by known detection means and as described herein.

[0080] In vivo administration to a human subject or an animal model can be by any of many standard means for administering viruses, depending upon the target organ, tissue or cell. Virus particles can be administered orally, parenterally (e.g., intravenously), by intramuscular injection, by direct tissue or organ injection, by intraperitoneal injection, topically, transdermally, or the like. Viral nucleic acids (non-encapsidated) can be administered, e.g., as a complex with cationic liposomes, or encapsulated in anionic liposomes. Compositions can include various amounts of the selected viral particle or non-encapsidated viral nucleic acid in combination with a pharmaceutically acceptable carrier and, in addition, if desired, may include other medicinal agents, pharmaceutical agents, carriers, adjuvants, diluents, etc. Parental administration, if used, is generally characterized by injection. Injectables can be prepared in conventional forms, either as liquid solutions or suspensions, solid forms suitable for solution or suspension in liquid prior to injection, or as emulsions. Dosages will depend upon the mode of administration, the disease or condition to be treated, and the individual subject's condition, but will be that dosage typical for and used in administration of other AAV vectors, such as AAV2 vectors. Often a single dose can be sufficient; however, the dose can be repeated if desirable.

[0081] The present invention further provides a method of delivering a nucleic acid to a cell in a subject having antibodies to AAV2 comprising administering to the subject an AAV4 particle comprising the nucleic acid, thereby delivering the nucleic acid to a cell in the subject. A subject that has antibodies to AAV2 can readily be determined by any of several known means, such as contacting AAV2 protein(s) with an antibody-containing sample, such as blood, from a subject and detecting an antigen-antibody reaction in the sample. Delivery of the AAV4 particle can be by either ex vivo or in vivo administration as herein described. Thus, a subject who might have an adverse immunogenic reaction to a vector administered in an AAV2 viral particle can have a desired nucleic acid delivered using an AAV4 particle. This delivery system can be particularly useful for subjects who have received therapy utilizing AAV2 particles in the past and have developed antibodies to AAV2. An AAV4 regimen can now be substituted to deliver the desired nucleic acid.

STATEMENT OF UTILITY

[0082] The present invention provides recombinant vectors based on AAV4. Such vectors may be useful for transducing erythroid progenitor cells which is very inefficient with AAV2 based vectors. In addition to transduction of other cell types, transduction of erythroid cells would be useful for the treatment of cancer and genetic diseases which can be corrected by bone marrow transplants using matched donors. Some examples of this type of treatment include, but are not limited to, the introduction of a therapeutic gene such as genes encoding interferons, interleukins, tumor necrosis factors, adenosine deaminase, cellular growth factors such as lymphokines, blood coagulation factors such as factor VIII and IX, cholesterol metabolism uptake and transport protein such as EpoE and LDL receptor, and antisense sequences to inhibit viral replication of, for example, hepatitis or HIV.

[0083] The present invention provides a vector comprising the AAV4 virus as well as AAV4 viral particles. While AAV4 is similar to AAV2, the two viruses are found herein to be physically and genetically distinct. These differences endow AAV4 with some unique advantages which better suit it as a vector for gene therapy. For example, the wt AAV4 genome is larger than AAV2, allowing for efficient encapsidation of a larger recombinant genome. Furthermore, wt AAV4 particles have a greater buoyant density than AAV2 particles and therefore are more easily separated from contaminating helper virus and empty AAV particles than AAV2-based particles.

[0084] Furthermore, as shown herein, AAV4 capsid protein is distinct from AAV2 capsid protein and exhibits different tissue tropism. AAV2 and AAV4 are shown herein to utilize distinct cellular receptors. AAV2 and AAV4 have been shown to be serologically distinct and thus, in a gene therapy application, AAV4 would allow for transduction of a patient who already possesses neutralizing antibodies to AAV2 either as a result of natural immunological defense or from prior exposure to AAV2 vectors.

[0085] The present invention is more particularly described in the following examples which are intended as illustrative only since numerous modifications and variations therein will be apparent to those skilled in the art.

EXAMPLES

[0086] To understand the nature of AAV4 virus and to determine its usefulness as a vector for gene transfer, it was cloned and sequenced.

[0087] Cell Culture and Virus Propagation

[0088] Cos and HeLa cells were maintained as monolayer cultures in D10 medium (Dulbecco's modified Eagle's medium containing 10% fetal calf serum, 100 μg/ml penicillin, 100 units/ml streptomycin and IX Fungizone as recommended by the manufacturer; (GIBCO, Gaithersburg, Md., U.S.A.) . All other cell types were grown under standard conditions which have been previously reported. AAV4 stocks were obtained from American Type Culture Collection #VR-64 6.

[0089] Virus was produced as previously described for AAV2, using the Beta galactosidase vector plasmid and a helper plasmid containing the AAV4 Rep and Cap genes (9). The helper plasmid was constructed in such a way as not to allow any homologous sequence between the helper and vector plasmids. This step was taken to minimize the potential for wild-type (wt) particle formation by homologous recombination.

[0090] Virus was isolated from 5×10⁷ cos cells by CsCl banding (9), and the distribution of Beta galactosidase genomes across the genome was determined by DNA dot blots of aliquots of gradient fractions. The majority of packaged genomes were found in fractions with a density of 1.43 which is similar to that reported for wt AAV4. This preparation of virus yielded 2.5×10¹¹ particles or 5000 particles/producer cell. In comparison AAV2 isolated and CsCl banded from 8×10⁷ cells yielded 1.2×10¹¹ particles or 1500 particles/producer cell. Thus, typical yields of rAAV4 particles/producer cell were 3-5 fold greater than that of rAAV2 particles.

[0091] DNA Cloning and Sequencing and Analysis

[0092] In order to clone the genome of AAV4, viral lysate was amplified in cos cells and then HeLa cells with the resulting viral particles isolated by CsCl banding. DNA dot blots of aliquots of the gradient fractions indicated that peak genomes were contained in fractions with a density of 1.41-1.45. This is very similar to the buoyant density previously reported for AAV4 (29). Analysis of annealed DNA obtained from these fractions indicated a major species of 4.8 kb in length which upon restriction analysis gave bands similar in size to those previously reported. Additional restriction analysis indicated the presence of BssHII restriction sites near the ends of the DNA. Digestion with BssHII yielded a 4.5 kb fragment which was then cloned into Bluescript SKII+ and two independent clones were sequenced.

[0093] The viral sequence is now available through Genebank, accession number U89790. DNA sequence was determined using an ABI 373A automated sequencer and the FS dye terminator chemistry. Both strands of the plasmids were sequenced and confirmed by sequencing of a second clone. As further confirmation of the authenticity of the sequence, bases 91-600 were PCR amplified from the original seed material and directly sequenced. The sequence of this region, which contains a 56 base insertion compared to AAV2 and 3, was found to be identical to that derived from the cloned material. The ITR was cloned using Deep Vent Polymerase (New England Biolabs) according to the manufactures instructions using the following primers, primer 1: 5′TCTAGTCTAGACTTGGCCACTCCCTCTCTGCGCGC (SEQ ID NO:21); primer 2: 51 AGGCCTTAAGAGCAGTCGTCCACCACCTTGTTCC (SEQ ID NO:22). Cycling conditions were 97° C. 20 sec, 65° C. 30 sec. 75° C. 1 min for 35 rounds. Following the PCR reaction, the mixture was treated with XbaI and EcoRI endonucleases and the amplified band purified by agarose gel electrophoresis. The recovered DNA fragment was ligated into Bluescript SKII+ (Stratagene) and transformed into competent Sure strain bacteria (Stratagene). The helper plasmid (pSV40oriAAV₄₋₂) used for the production of recombinant virus, which contains the rep and cap genes of AAV4, was produced by PCR with Pfu polymerase (Stratagene) according to the manufactures instructions. The amplified sequence, nt 216-4440, was ligated into a plasmid that contains the SV40 origin of replication previously described (9, 10). Cycling conditions were 95° C. 30 sec, 55° C. 30 sec, 72° C. 3 min for 20 rounds. The final clone was confirmed by sequencing. The βgal reporter vector has been described previously (9, 10).

[0094] Sequencing of this fragment revealed two open reading frames (ORF) instead of only one as previously suggested. In addition to the previously identified Capsid ORF in the right-hand side of the genome, an additional ORF is present on the left-hand side. Computer analysis indicated that the left-hand ORF has a high degree of homology to the Rep gene of AAV2. At the amino acid level the ORF is 90% identical to that of AAV2 with only 5% of the changes being non-conserved (SEQ ID NO:2). In contrast, the right ORF is only 62% identical at the amino acid level when compared to the corrected AAV2 sequence. While the internal start site of VP2 appears to be conserved, the start site for VP3 is in the middle of one of the two blocks of divergent sequence. The second divergent block is in the middle of VP3. By using three dimensional structure analysis of the canine parvovirus and computer aided sequence comparisons, regions of AAV2 which might be exposed on the surface of the virus have been identified. Comparison of the AAV2 and AAV4 sequences indicates that these regions are not well conserved between the two viruses and suggests altered tissue tropism for the two viruses.

[0095] Comparison of the p5 promoter region of the two viruses shows a high degree of conservation of known functional elements (SEQ ID NO:7). Initial work by Chang et al. identified two YY1 binding sites at −60 and +1 and a TATA Box at −30 which are all conserved between AAV2 and AAV4 (4). A binding site for the Rep has been identified in the p5 promoter at −17 and is also conserved (24). The only divergence between the two viruses in this region appears to be in the sequence surrounding these elements. AAV4 also contains an additional 56 bases in this region between the p5 promoter and the TRS (nt 209-269). Based on its positioning in the viral genome and efficient use of the limited genome space, this sequence may possess some promoter activity or be involved in rescue, replication or packaging of the virus.

[0096] The inverted terminal repeats were cloned by PCR using a probe derived from the terminal resolution site (TRS)of the BssHII fragment and a primer in the Rep ORF. The TRS is a sequence at the end of the stem of the ITR and the reverse compliment of TRS sequence was contained within the BssHII fragment. The resulting fragments were cloned and found to contain a number of sequence changes compared to AAV2. However, these changes were found to be complementary and did not affect the ability of this region to fold into a hairpin structure (FIG. 2). While the TRS site was conserved between AAV2 and AAV4 the Rep binding site contained two alterations which expand the binding site from 3 GAGC repeats to 4. The first two repeats in AAV4 both contain a T in the fourth position instead of a C. This type of repeat is present in the p5 promoter and is present in the consensus sequence that has been proposed for Rep binding (10) and its expansion may affect its affinity for Rep. Methylation interference data has suggested the importance of the CTTTG motif found at the tip of one palindrome in Rep binding with the underlined T residues clearly affecting Rep binding to both the flip and flop forms. While most of this motif is conserved in AAV4 the middle T residue is changed to a C (33).

[0097] Hemagglutination Assays

[0098] Hemagglutination was measured essentially as described previously (18). Serial two fold dilutions of virus in Veronal-buffered saline were mixed with an equal volume of 0.4% human erythrocytes (type 0) in plastic U bottom 96 well plates. The reaction was complete after a 2 hr incubation at 8° C. HA units (HAU) are defined as the reciprocal of the dilution causing 50% hemagglutination.

[0099] The results show that both the wild type and recombinant AAV4 viruses can hemagglutinate human red blood cells (RBCS) with HA titers of approximately 1024 HAU/μl and 512 HAU/μl respectively. No HA activity was detected with AAV type 3 or recombinant AAV type 2 as well as the helper adenovirus. If the temperature was raised to 22° C., HA activity decreased 32-fold. Comparison of the viral particle number per RBC at the end point dilution indicated that approximately 1-10 particles per RBC were required for hemagglutination. This value is similar to that previously reported (18).

[0100] Tissue Tropism Analysis

[0101] The sequence divergence in the capsid proteins ORF which are predicted to be exposed on the surface of the virus may result in an altered binding specificity for AAV4 compared to AAV2. Very little is known about the tissue tropism of any dependovirus. While it had been shown to hemagglutinate human, guinea pig, and sheep erythrocytes, it is thought to be exclusively a simian virus (18). Therefore, to examine AAV4 tissue tropism and its species specificity, recombinant AAV4 particles which contained the gene for nuclear localized Beta galactosidase were constructed. Because of the similarity in genetic organization of AAV4 and AAV2, it was determined whether AAV4 particles could be constructed containing a recombinant genome. Furthermore, because of the structural similarities of the AAV type 2 and type 4 ITRs, a genome containing AAV2 ITRs which had been previously described was used.

[0102] Tissue Tropism Analysis 1.

[0103] To study AAV transduction, a variety of cell lines were transduced with 5 fold serial dilutions of either recombinant AAV2 or AAV4 particles expressing the gene for nuclear localized Beta galactosidase activity (Table 1). Approximately 4×10⁴ cells were exposed to virus in 0.5 ml serum free media for 1 hour and then 1 ml of the appropriate complete media was added and the cells were incubated for 48-60 hours. The cells were then fixed and stained for β-galactosidase activity with 5-Bromo-4-Chloro-3-Indolyl-β-D-galactopyranoside (Xgal) (ICN Biomedicals) (36). Biological titers were determined by counting the number of positive cells in the different dilutions using a calibrated microscope ocular (3.1 mm²) then multiplying by the area of the well and the dilution of the virus. Typically dilutions which gave 1-10 positive cells per field (100-1000 positive cells per 2 cm well) were used for titer determination. Titers were determined by the average number of cells in a minimum of 10 fields/well.

[0104] To examine difference in tissue tropism, a number of cell lines were transduced with serial dilutions of either AAV4 or AAV2 and the biological titers determined. As shown in Table 1, when Cos cells were transduced with a similar number of viral particles, a similar level of transduction was observed with AAV2 and AAV4. However, other cell lines exhibited differential transducibility by AAV2 or AAV4. Transduction of the human colon adenocarcinoma cell line SW480 with AAV2 was over 100 times higher than that obtained with AAV4. Furthermore, both vectors transduced SW1116, SW1463 and NIH3T3 cells relatively poorly. TABLE 1 Cell type AAV2 AAV4 Cos 4.5 × 10⁷ 1.9 × 10⁷ SW 480 3.8 × 10⁶ 2.8 × 10⁴ SW 1116 5.2 × 10⁴   8 × 10³ SW1463 8.8 × 10⁴   8 × 10³ SW620 8.8 × 10⁴ ND NIH 3T3   2 × 10⁴   8 × 10³

[0105] Tissue Tropism Analysis 2.

[0106] A. Transduction of Cells.

[0107] Exponentially growing cells (2×10⁴) were plated in each well of a 12 well plate and transduced with serial dilutions of virus in 200 μl of medium for 1 hr. After this period, 800 μl of additional medium was added and incubated for 48 hrs. The cells were then fixed and stained for β-galactosidase activity overnight with 5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside (Xgal) (ICN Biomedicals) (36). No endogenous β-galactosidase activity was visible after 24 hr incubation in Xgal solution. Infectious titers were determined by counting the number of positive cells in the different dilutions using a calibrated microscope ocular (diameter 3.1 mm²) then multiplying by the area of the well and the dilution of the virus. Titers were determined by the average number of cells in a minimum of 10 fields/well.

[0108] As shown in Table 2, cos cells transduced with equivalent amounts of rAAV2 and rAAV4particles resulted in similar transduction levels. However, other cell lines exhibited differential transducibility. Transduction of the human colon adenocarcinoma cell line, SW480, with rAAV2 was 60 times higher than that obtained with rAAV4. HeLa and SW620 cells were also transduced more efficiently with rAAV2 than rAAV4. In contrast, transduction of primary rat brain cultures exhibited a greater transduction of glial and neuronal cells with rAAV4 compared to rAAV2. Because of the heterogeneous nature of the cell population in the rat brain cultures, only relative transduction efficiencies are reported (Table 2).

[0109] As a control for adenovirus contamination of the viral preparations cos and HeLa cells were coinfected with RAAV and adenovirus then stained after 24 hr. While the titer of rAAV2 increased in the presence of Ad in both cos and HeLa, adenovirus only increased the titer in the cos cells transduced with rAAV4 and not the HeLa cells, suggesting the difference in transduction efficiencies is not the result of adenovirus contamination. Furthermore, both vectors transduced SW1116, SW1463, NIH3T3 and monkey fibroblasts FL2 cells very poorly. Thus AAV4 may utilize a cellular receptor distinct from that of AAV2. TABLE 2 CELL TYPE AAV2 AAV4 Primary Rat Brain 1 4.3 · 0.7 cos  4.2 × 10⁷ · 4.6 × 10⁶ 2.2 × 10⁷ · 2.5 × 10⁶ SW 480 7.75 × 10⁶ · 1.7 × 10⁶ 1.3 × 10⁵ · 6.8 × 10⁴ HeLa  2.1 × 10⁷ · 1 × 10⁶ 1.3 × 10⁶ · 1 × 10⁵ SW620  1.2 × 10⁵ · 3.9 × 10⁴   4 × 10⁴ KLEB  1.2 × 10⁵ · 3.5 × 10⁴   9 × 10⁴ · 1.4 × 10⁴ HB  5.6 × 10⁵ · 2 × 10⁵ 3.8 × 10⁴ · 1.8 × 10⁴ SW1116  5.2 × 10⁴   8 × 10³ SW1463  8.8 × 10⁴   8 × 10³ NIH 3T3   3 × 10³   2 × 10³

[0110] B. Competition Assay.

[0111] Cos cells were plated at 2×10⁴/well in 12 well plates 12-24 hrs prior to transduction. Cells were transduced with 0.5×10⁷ particles of rAAV2 or rAAV4 (containing the LacZ gene) in 200 μl of DMEM and increasing amounts of rAAV2 containing the gene for the human coagulation factor IX. Prior to transduction the CsCl was removed from the virus by dialysis against isotonic saline. After 1 hr incubation with the recombinant virus the culture medium was supplemented with complete medium and allowed to incubate for 48-60 hrs. The cells were then stained and counted as described above.

[0112] AAV4 utilization of a cellular receptor distinct from that of AAV2 was further examined by cotransduction experiments with rAAV2 and rAAV4. Cos cells were transduced with an equal number of rAAV2 or rAAV4 particles containing the LacZ gene and increasing amounts of rAAV2 particles containing the human coagulation factor IX gene (rAAV2FIX) . At a 72:1 ratio of rAAV2FIX:rAAV4LacZ only a two-fold effect on the level of rAAV4LacZ transduction was obtained (FIG. 3). However this same ratio of rAAV2FIX:rAAV2LacZ reduced the transduction efficiency of rAAV2LacZ approximately 10 fold. Comparison of the 50% inhibition points for the two viruses indicated a 7 fold difference in sensitivity.

[0113] C. Trypsinization of Cells.

[0114] An 80% confluent monolayer of cos cells (1×10⁷) was treated with 0.05% trypsin/0.02% versene solution (Biofluids) for 3-5 min at 37□ C. Following detachment the trypsin was inactivated by the addition of an equal volume of media containing 10% fetal calf serum. The cells were then further diluted to a final concentration of 1×10⁴/ml. One ml of cells was plated in a 12 well dish and incubated with virus at a multiplicity of infection (MOI) of 260 for 1-2 hrs. Following attachment of the cells the media containing the virus was removed, the cells washed and fresh media was added. Control cells were plated at the same time but were not transduced until the next day. Transduction conditions were done as described above for the trypsinized cell group. The number of transduced cells was determined by staining 48-60 hrs post transduction and counted as described above.

[0115] Previous research had shown that binding and infection of AAV2 is inhibited by trypsin treatment of cells (26). Transduction of cos cells with rAAV21acZ gene was also inhibited by trypsin treatment prior to transduction (FIG. 4). In contrast trypsin treatment had a minimal effect on rAAV41acZ transduction. This result and the previous competition experiment are both consistent with the utilization of distinct cellular receptors for AAV2 and AAV4.

[0116] AAV4 is a distinct virus based on sequence analysis, physical properties of the virion, hemagglutination activity, and tissue tropism. The sequence data indicates that AAV4 is a distinct virus from that of AAV2. In contrast to original reports, AAV4 contains two open reading frames which code for either Rep proteins or Capsid proteins. AAV4 contains additional sequence upstream of the p5 promoter which may affect promoter activity, packaging or particle stability. Furthermore, AAV4 contains an expanded Rep binding site in its ITR which could alter its activity as an origin of replication or promoter. The majority of the differences in the Capsid proteins lies in regions which have been proposed to be on the exterior surface of the parvovirus. These changes are most likely responsible for the lack of cross reacting antibodies, hemagglutinate activity, and the altered tissue tropism compared to AAV2. Furthermore, in contrast to previous reports AAV4 is able to transduce human as well as monkey cells.

[0117] Throughout this application, various publications are referenced. The disclosures of these publications in their entireties are hereby incorporated by reference into this application in order to more fully describe the state of the art to which this invention pertains.

[0118] Although the present process has been described with reference to specific details of certain embodiments thereof, it is not intended that such details should be regarded as limitations upon the scope of the invention except as and to the extent that they are included in the accompanying claims.

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1 22 4768 base pairs nucleic acid double linear DNA (genomic) AAV4 genome 1 TTGGCCACTC CCTCTATGCG CGCTCGCTCA CTCACTCGGC CCTGGAGACC AAAGGTCTCC 60 AGACTGCCGG CCTCTGGCCG GCAGGGCCGA GTGAGTGAGC GAGCGCGCAT AGAGGGAGTG 120 GCCAACTCCA TCATCTAGGT TTGCCCACTG ACGTCAATGT GACGTCCTAG GGTTAGGGAG 180 GTCCCTGTAT TAGCAGTCAC GTGAGTGTCG TATTTCGCGG AGCGTAGCGG AGCGCATACC 240 AAGCTGCCAC GTCACAGCCA CGTGGTCCGT TTGCGACAGT TTGCGACACC ATGTGGTCAC 300 GAGGGTATAT AACCGCGAGT GAGCCAGCGA GGAGCTCCAT TTTGCCCGCG AATTTTGAAC 360 GAGCAGCAGC CATGCCGGGG TTCTACGAGA TCGTGCTGAA GGTGCCCAGC GACCTGGACG 420 AGCACCTGCC CGGCATTTCT GACTCTTTTG TGAGCTGGGT GGCCGAGAAG GAATGGGAGC 480 TGCCGCCGGA TTCTGACATG GACTTGAATC TGATTGAGCA GGCACCCCTG ACCGTGGCCG 540 AAAAGCTGCA ACGCGAGTTC CTGGTCGAGT GGCGCCGCGT GAGTAAGGCC CCGGAGGCCC 600 TCTTCTTTGT CCAGTTCGAG AAGGGGGACA GCTACTTCCA CCTGCACATC CTGGTGGAGA 660 CCGTGGGCGT CAAATCCATG GTGGTGGGCC GCTACGTGAG CCAGATTAAA GAGAAGCTGG 720 TGACCCGCAT CTACCGCGGG GTCGAGCCGC AGCTTCCGAA CTGGTTCGCG GTGACCAAGA 780 CGCGTAATGG CGCCGGAGGC GGGAACAAGG TGGTGGACGA CTGCTACATC CCCAACTACC 840 TGCTCCCCAA GACCCAGCCC GAGCTCCAGT GGGCGTGGAC TAACATGGAC CAGTATATAA 900 GCGCCTGTTT GAATCTCGCG GAGCGTAAAC GGCTGGTGGC GCAGCATCTG ACGCACGTGT 960 CGCAGACGCA GGAGCAGAAC AAGGAAAACC AGAACCCCAA TTCTGACGCG CCGGTCATCA 1020 GGTCAAAAAC CTCCGCCAGG TACATGGAGC TGGTCGGGTG GCTGGTGGAC CGCGGGATCA 1080 CGTCAGAAAA GCAATGGATC CAGGAGGACC AGGCGTCCTA CATCTCCTTC AACGCCGCCT 1140 CCAACTCGCG GTCACAAATC AAGGCCGCGC TGGACAATGC CTCCAAAATC ATGAGCCTGA 1200 CAAAGACGGC TCCGGACTAC CTGGTGGGCC AGAACCCGCC GGAGGACATT TCCAGCAACC 1260 GCATCTACCG AATCCTCGAG ATGAACGGGT ACGATCCGCA GTACGCGGCC TCCGTCTTCC 1320 TGGGCTGGGC GCAAAAGAAG TTCGGGAAGA GGAACACCAT CTGGCTCTTT GGGCCGGCCA 1380 CGACGGGTAA AACCAACATC GCGGAAGCCA TCGCCCACGC CGTGCCCTTC TACGGCTGCG 1440 TGAACTGGAC CAATGAGAAC TTTCCGTTCA ACGATTGCGT CGACAAGATG GTGATCTGGT 1500 GGGAGGAGGG CAAGATGACG GCCAAGGTCG TAGAGAGCGC CAAGGCCATC CTGGGCGGAA 1560 GCAAGGTGCG CGTGGACCAA AAGTGCAAGT CATCGGCCCA GATCGACCCA ACTCCCGTGA 1620 TCGTCACCTC CAACACCAAC ATGTGCGCGG TCATCGACGG AAACTCGACC ACCTTCGAGC 1680 ACCAACAACC ACTCCAGGAC CGGATGTTCA AGTTCGAGCT CACCAAGCGC CTGGAGCACG 1740 ACTTTGGCAA GGTCACCAAG CAGGAAGTCA AAGACTTTTT CCGGTGGGCG TCAGATCACG 1800 TGACCGAGGT GACTCACGAG TTTTACGTCA GAAAGGGTGG AGCTAGAAAG AGGCCCGCCC 1860 CCAATGACGC AGATATAAGT GAGCCCAAGC GGGCCTGTCC GTCAGTTGCG CAGCCATCGA 1920 CGTCAGACGC GGAAGCTCCG GTGGACTACG CGGACAGGTA CCAAAACAAA TGTTCTCGTC 1980 ACGTGGGTAT GAATCTGATG CTTTTTCCCT GCCGGCAATG CGAGAGAATG AATCAGAATG 2040 TGGACATTTG CTTCACGCAC GGGGTCATGG ACTGTGCCGA GTGCTTCCCC GTGTCAGAAT 2100 CTCAACCCGT GTCTGTCGTC AGAAAGCGGA CGTATCAGAA ACTGTGTCCG ATTCATCACA 2160 TCATGGGGAG GGCGCCCGAG GTGGCCTGCT CGGCCTGCGA ACTGGCCAAT GTGGACTTGG 2220 ATGACTGTGA CATGGAACAA TAAATGACTC AAACCAGATA TGACTGACGG TTACCTTCCA 2280 GATTGGCTAG AGGACAACCT CTCTGAAGGC GTTCGAGAGT GGTGGGCGCT GCAACCTGGA 2340 GCCCCTAAAC CCAAGGCAAA TCAACAACAT CAGGACAACG CTCGGGGTCT TGTGCTTCCG 2400 GGTTACAAAT ACCTCGGACC CGGCAACGGA CTCGACAAGG GGGAACCCGT CAACGCAGCG 2460 GACGCGGCAG CCCTCGAGCA CGACAAGGCC TACGACCAGC AGCTCAAGGC CGGTGACAAC 2520 CCCTACCTCA AGTACAACCA CGCCGACGCG GAGTTCCAGC AGCGGCTTCA GGGCGACACA 2580 CCGTTTGGGG GCAACCTCGG CAGAGCAGTC TTCCAGGCCA AAAAGAGGGT TCTTGAACCT 2640 CTTGGTCTGG TTGAGCAAGC GGGTGAGACG GCTCCTGGAA AGAAGAGACC GTTGATTGAA 2700 TCCCCCCAGC AGCCCGACTC CTCCACGGGT ATCGGCAAAA AAGGCAAGCA GCCGGCTAAA 2760 AAGAAGCTCG TTTTCGAAGA CGAAACTGGA GCAGGCGACG GACCCCCTGA GGGATCAACT 2820 TCCGGAGCCA TGTCTGATGA CAGTGAGATG CGTGCAGCAG CTGGCGGAGC TGCAGTCGAG 2880 GGSGGACAAG GTGCCGATGG AGTGGGTAAT GCCTCGGGTG ATTGGCATTG CGATTCCACC 2940 TGGTCTGAGG GCCACGTCAC GACCACCAGC ACCAGAACCT GGGTCTTGCC CACCTACAAC 3000 AACCACCTNT ACAAGCGACT CGGAGAGAGC CTGCAGTCCA ACACCTACAA CGGATTCTCC 3060 ACCCCCTGGG GATACTTTGA CTTCAACCGC TTCCACTGCC ACTTCTCACC ACGTGACTGG 3120 CAGCGACTCA TCAACAACAA CTGGGGCATG CGACCCAAAG CCATGCGGGT CAAAATCTTC 3180 AACATCCAGG TCAAGGAGGT CACGACGTCG AACGGCGAGA CAACGGTGGC TAATAACCTT 3240 ACCAGCACGG TTCAGATCTT TGCGGACTCG TCGTACGAAC TGCCGTACGT GATGGATGCG 3300 GGTCAAGAGG GCAGCCTGCC TCCTTTTCCC AACGACGTCT TTATGGTGCC CCAGTACGCC 3360 TACTGTGGAC TGGTGACCGG CAACACTTCG CAGCAACAGA CTGACAGAAA TGCCTTCTAC 3420 TGCCTGGAGT ACTTTCCTTC GCAGATGCTG CGGACTGGCA ACAACTTTGA AATTACGTAC 3480 AGTTTTGAGA AGGTGCCTTT CCACTCGATG TACGCGCACA GCCAGAGCCT GGACCGGCTG 3540 ATGAACCCTC TCATCGACCA GTACCTGTGG GGACTGCAAT CGACCACCAC CGGAACCACC 3600 CTGAATGCCG GGACTGCCAC CACCAACTTT ACCAAGCTGC GGCCTACCAA CTTTTCCAAC 3660 TTTAAAAAGA ACTGGCTGCC CGGGCCTTCA ATCAAGCAGC AGGGCTTCTC AAAGACTGCC 3720 AATCAAAACT ACAAGATCCC TGCCACCGGG TCAGACAGTC TCATCAAATA CGAGACGCAC 3780 AGCACTCTGG ACGGAAGATG GAGTGCCCTG ACCCCCGGAC CTCCAATGGC CACGGCTGGA 3840 CCTGCGGACA GCAAGTTCAG CAACAGCCAG CTCATCTTTG CGGGGCCTAA ACAGAACGGC 3900 AACACGGCCA CCGTACCCGG GACTCTGATC TTCACCTCTG AGGAGGAGCT GGCAGCCACC 3960 AACGCCACCG ATACGGACAT GTGGGGCAAC CTACCTGGCG GTGACCAGAG CAACAGCAAC 4020 CTGCCGACCG TGGACAGACT GACAGCCTTG GGAGCCGTGC CTGGAATGGT CTGGCAAAAC 4080 AGAGACATTT ACTACCAGGG TCCCATTTGG GCCAAGATTC CTCATACCGA TGGACACTTT 4140 CACCCCTCAC CGCTGATTGG TGGGTTTGGG CTGAAACACC CGCCTCCTCA AATTTTTATC 4200 AAGAACACCC CGGTACCTGC GAATCCTGCA ACGACCTTCA GCTCTACTCC GGTAAACTCC 4260 TTCATTACTC AGTACAGCAC TGGCCAGGTG TCGGTGCAGA TTGACTGGGA GATCCAGAAG 4320 GAGCGGTCCA AACGCTGGAA CCCCGAGGTC CAGTTTACCT CCAACTACGG ACAGCAAAAC 4380 TCTCTGTTGT GGGCTCCCGA TGCGGCTGGG AAATACACTG AGCCTAGGGC TATCGGTACC 4440 CGCTACCTCA CCCACCACCT GTAATAACCT GTTAATCAAT AAACCGGTTT ATTCGTTTCA 4500 GTTGAACTTT GGTCTCCGTG TCCTTCTTAT CTTATCTCGT TTCCATGGCT ACTGCGTACA 4560 TAAGCAGCGG CCTGCGGCGC TTGCGCTTCG CGGTTTACAA CTGCCGGTTA ATCAGTAACT 4620 TCTGGCAAAC CATGATGATG GAGTTGGCCA CTCCCTCTAT GCGCGCTCGC TCACTCACTC 4680 GGCCCTGGAG ACCAAAGGTC TCCAGACTGC CGGCCTCTGG CCGGCAGGGC CGAGTGAGTG 4740 AGCGAGCGCG CATAGAGGGA GTGGCCAA 4768 623 amino acids amino acid linear protein AAV4 Rep protein (full length) 2 Met Pro Gly Phe Tyr Glu Ile Val Leu Lys Val Pro Ser Asp Leu Asp 1 5 10 15 Glu His Leu Pro Gly Ile Ser Asp Ser Phe Val Ser Trp Val Ala Glu 20 25 30 Lys Glu Trp Glu Leu Pro Pro Asp Ser Asp Met Asp Leu Asn Leu Ile 35 40 45 Glu Gln Ala Pro Leu Thr Val Ala Glu Lys Leu Gln Arg Glu Phe Leu 50 55 60 Val Glu Trp Arg Arg Val Ser Lys Ala Pro Glu Ala Leu Phe Phe Val 65 70 75 80 Gln Phe Glu Lys Gly Asp Ser Tyr Phe His Leu His Ile Leu Val Glu 85 90 95 Thr Val Gly Val Lys Ser Met Val Val Gly Arg Tyr Val Ser Gln Ile 100 105 110 Lys Glu Lys Leu Val Thr Arg Ile Tyr Arg Gly Val Glu Pro Gln Leu 115 120 125 Pro Asn Trp Phe Ala Val Thr Lys Thr Arg Asn Gly Ala Gly Gly Gly 130 135 140 Asn Lys Val Val Asp Asp Cys Tyr Ile Pro Asn Tyr Leu Leu Pro Lys 145 150 155 160 Thr Gln Pro Glu Leu Gln Trp Ala Trp Thr Asn Met Asp Gln Tyr Ile 165 170 175 Ser Ala Cys Leu Asn Leu Ala Glu Arg Lys Arg Leu Val Ala Gln His 180 185 190 Leu Thr His Val Ser Gln Thr Gln Glu Gln Asn Lys Glu Asn Gln Asn 195 200 205 Pro Asn Ser Asp Ala Pro Val Ile Arg Ser Lys Thr Ser Ala Arg Tyr 210 215 220 Met Glu Leu Val Gly Trp Leu Val Asp Arg Gly Ile Thr Ser Glu Lys 225 230 235 240 Gln Trp Ile Gln Glu Asp Gln Ala Ser Tyr Ile Ser Phe Asn Ala Ala 245 250 255 Ser Asn Ser Arg Ser Gln Ile Lys Ala Ala Leu Asp Asn Ala Ser Lys 260 265 270 Ile Met Ser Leu Thr Lys Thr Ala Pro Asp Tyr Leu Val Gly Gln Asn 275 280 285 Pro Pro Glu Asp Ile Ser Ser Asn Arg Ile Tyr Arg Ile Leu Glu Met 290 295 300 Asn Gly Tyr Asp Pro Gln Tyr Ala Ala Ser Val Phe Leu Gly Trp Ala 305 310 315 320 Gln Lys Lys Phe Gly Lys Arg Asn Thr Ile Trp Leu Phe Gly Pro Ala 325 330 335 Thr Thr Gly Lys Thr Asn Ile Ala Glu Ala Ile Ala His Ala Val Pro 340 345 350 Phe Tyr Gly Cys Val Asn Trp Thr Asn Glu Asn Phe Pro Phe Asn Asp 355 360 365 Cys Val Asp Lys Met Val Ile Trp Trp Glu Glu Gly Lys Met Thr Ala 370 375 380 Lys Val Val Glu Ser Ala Lys Ala Ile Leu Gly Gly Ser Lys Val Arg 385 390 395 400 Val Asp Gln Lys Cys Lys Ser Ser Ala Gln Ile Asp Pro Thr Pro Val 405 410 415 Ile Val Thr Ser Asn Thr Asn Met Cys Ala Val Ile Asp Gly Asn Ser 420 425 430 Thr Thr Phe Glu His Gln Gln Pro Leu Gln Asp Arg Met Phe Lys Phe 435 440 445 Glu Leu Thr Lys Arg Leu Glu His Asp Phe Gly Lys Val Thr Lys Gln 450 455 460 Glu Val Lys Asp Phe Phe Arg Trp Ala Ser Asp His Val Thr Glu Val 465 470 475 480 Thr His Glu Phe Tyr Val Arg Lys Gly Gly Ala Arg Lys Arg Pro Ala 485 490 495 Pro Asn Asp Ala Asp Ile Ser Glu Pro Lys Arg Ala Cys Pro Ser Val 500 505 510 Ala Gln Pro Ser Thr Ser Asp Ala Glu Ala Pro Val Asp Tyr Ala Asp 515 520 525 Arg Tyr Gln Asn Lys Cys Ser Arg His Val Gly Met Asn Leu Met Leu 530 535 540 Phe Pro Cys Arg Gln Cys Glu Arg Met Asn Gln Asn Val Asp Ile Cys 545 550 555 560 Phe Thr His Gly Val Met Asp Cys Ala Glu Cys Phe Pro Val Ser Glu 565 570 575 Ser Gln Pro Val Ser Val Val Arg Lys Arg Thr Tyr Gln Lys Leu Cys 580 585 590 Pro Ile His His Ile Met Gly Arg Ala Pro Glu Val Ala Cys Ser Ala 595 600 605 Cys Glu Leu Ala Asn Val Asp Leu Asp Asp Cys Asp Met Glu Gln 610 615 620 1872 base pairs nucleic acid double linear DNA (genomic) CDS 1..1872 AAV4 Rep gene (full length) 3 ATG CCG GGG TTC TAC GAG ATC GTG CTG AAG GTG CCC AGC GAC CTG GAC 48 Met Pro Gly Phe Tyr Glu Ile Val Leu Lys Val Pro Ser Asp Leu Asp 1 5 10 15 GAG CAC CTG CCC GGC ATT TCT GAC TCT TTT GTG AGC TGG GTG GCC GAG 96 Glu His Leu Pro Gly Ile Ser Asp Ser Phe Val Ser Trp Val Ala Glu 20 25 30 AAG GAA TGG GAG CTG CCG CCG GAT TCT GAC ATG GAC TTG AAT CTG ATT 144 Lys Glu Trp Glu Leu Pro Pro Asp Ser Asp Met Asp Leu Asn Leu Ile 35 40 45 GAG CAG GCA CCC CTG ACC GTG GCC GAA AAG CTG CAA CGC GAG TTC CTG 192 Glu Gln Ala Pro Leu Thr Val Ala Glu Lys Leu Gln Arg Glu Phe Leu 50 55 60 GTC GAG TGG CGC CGC GTG AGT AAG GCC CCG GAG GCC CTC TTC TTT GTC 240 Val Glu Trp Arg Arg Val Ser Lys Ala Pro Glu Ala Leu Phe Phe Val 65 70 75 80 CAG TTC GAG AAG GGG GAC AGC TAC TTC CAC CTG CAC ATC CTG GTG GAG 288 Gln Phe Glu Lys Gly Asp Ser Tyr Phe His Leu His Ile Leu Val Glu 85 90 95 ACC GTG GGC GTC AAA TCC ATG GTG GTG GGC CGC TAC GTG AGC CAG ATT 336 Thr Val Gly Val Lys Ser Met Val Val Gly Arg Tyr Val Ser Gln Ile 100 105 110 AAA GAG AAG CTG GTG ACC CGC ATC TAC CGC GGG GTC GAG CCG CAG CTT 384 Lys Glu Lys Leu Val Thr Arg Ile Tyr Arg Gly Val Glu Pro Gln Leu 115 120 125 CCG AAC TGG TTC GCG GTG ACC AAG ACG CGT AAT GGC GCC GGA GGC GGG 432 Pro Asn Trp Phe Ala Val Thr Lys Thr Arg Asn Gly Ala Gly Gly Gly 130 135 140 AAC AAG GTG GTG GAC GAC TGC TAC ATC CCC AAC TAC CTG CTC CCC AAG 480 Asn Lys Val Val Asp Asp Cys Tyr Ile Pro Asn Tyr Leu Leu Pro Lys 145 150 155 160 ACC CAG CCC GAG CTC CAG TGG GCG TGG ACT AAC ATG GAC CAG TAT ATA 528 Thr Gln Pro Glu Leu Gln Trp Ala Trp Thr Asn Met Asp Gln Tyr Ile 165 170 175 AGC GCC TGT TTG AAT CTC GCG GAG CGT AAA CGG CTG GTG GCG CAG CAT 576 Ser Ala Cys Leu Asn Leu Ala Glu Arg Lys Arg Leu Val Ala Gln His 180 185 190 CTG ACG CAC GTG TCG CAG ACG CAG GAG CAG AAC AAG GAA AAC CAG AAC 624 Leu Thr His Val Ser Gln Thr Gln Glu Gln Asn Lys Glu Asn Gln Asn 195 200 205 CCC AAT TCT GAC GCG CCG GTC ATC AGG TCA AAA ACC TCC GCC AGG TAC 672 Pro Asn Ser Asp Ala Pro Val Ile Arg Ser Lys Thr Ser Ala Arg Tyr 210 215 220 ATG GAG CTG GTC GGG TGG CTG GTG GAC CGC GGG ATC ACG TCA GAA AAG 720 Met Glu Leu Val Gly Trp Leu Val Asp Arg Gly Ile Thr Ser Glu Lys 225 230 235 240 CAA TGG ATC CAG GAG GAC CAG GCG TCC TAC ATC TCC TTC AAC GCC GCC 768 Gln Trp Ile Gln Glu Asp Gln Ala Ser Tyr Ile Ser Phe Asn Ala Ala 245 250 255 TCC AAC TCG CGG TCA CAA ATC AAG GCC GCG CTG GAC AAT GCC TCC AAA 816 Ser Asn Ser Arg Ser Gln Ile Lys Ala Ala Leu Asp Asn Ala Ser Lys 260 265 270 ATC ATG AGC CTG ACA AAG ACG GCT CCG GAC TAC CTG GTG GGC CAG AAC 864 Ile Met Ser Leu Thr Lys Thr Ala Pro Asp Tyr Leu Val Gly Gln Asn 275 280 285 CCG CCG GAG GAC ATT TCC AGC AAC CGC ATC TAC CGA ATC CTC GAG ATG 912 Pro Pro Glu Asp Ile Ser Ser Asn Arg Ile Tyr Arg Ile Leu Glu Met 290 295 300 AAC GGG TAC GAT CCG CAG TAC GCG GCC TCC GTC TTC CTG GGC TGG GCG 960 Asn Gly Tyr Asp Pro Gln Tyr Ala Ala Ser Val Phe Leu Gly Trp Ala 305 310 315 320 CAA AAG AAG TTC GGG AAG AGG AAC ACC ATC TGG CTC TTT GGG CCG GCC 1008 Gln Lys Lys Phe Gly Lys Arg Asn Thr Ile Trp Leu Phe Gly Pro Ala 325 330 335 ACG ACG GGT AAA ACC AAC ATC GCG GAA GCC ATC GCC CAC GCC GTG CCC 1056 Thr Thr Gly Lys Thr Asn Ile Ala Glu Ala Ile Ala His Ala Val Pro 340 345 350 TTC TAC GGC TGC GTG AAC TGG ACC AAT GAG AAC TTT CCG TTC AAC GAT 1104 Phe Tyr Gly Cys Val Asn Trp Thr Asn Glu Asn Phe Pro Phe Asn Asp 355 360 365 TGC GTC GAC AAG ATG GTG ATC TGG TGG GAG GAG GGC AAG ATG ACG GCC 1152 Cys Val Asp Lys Met Val Ile Trp Trp Glu Glu Gly Lys Met Thr Ala 370 375 380 AAG GTC GTA GAG AGC GCC AAG GCC ATC CTG GGC GGA AGC AAG GTG CGC 1200 Lys Val Val Glu Ser Ala Lys Ala Ile Leu Gly Gly Ser Lys Val Arg 385 390 395 400 GTG GAC CAA AAG TGC AAG TCA TCG GCC CAG ATC GAC CCA ACT CCC GTG 1248 Val Asp Gln Lys Cys Lys Ser Ser Ala Gln Ile Asp Pro Thr Pro Val 405 410 415 ATC GTC ACC TCC AAC ACC AAC ATG TGC GCG GTC ATC GAC GGA AAC TCG 1296 Ile Val Thr Ser Asn Thr Asn Met Cys Ala Val Ile Asp Gly Asn Ser 420 425 430 ACC ACC TTC GAG CAC CAA CAA CCA CTC CAG GAC CGG ATG TTC AAG TTC 1344 Thr Thr Phe Glu His Gln Gln Pro Leu Gln Asp Arg Met Phe Lys Phe 435 440 445 GAG CTC ACC AAG CGC CTG GAG CAC GAC TTT GGC AAG GTC ACC AAG CAG 1392 Glu Leu Thr Lys Arg Leu Glu His Asp Phe Gly Lys Val Thr Lys Gln 450 455 460 GAA GTC AAA GAC TTT TTC CGG TGG GCG TCA GAT CAC GTG ACC GAG GTG 1440 Glu Val Lys Asp Phe Phe Arg Trp Ala Ser Asp His Val Thr Glu Val 465 470 475 480 ACT CAC GAG TTT TAC GTC AGA AAG GGT GGA GCT AGA AAG AGG CCC GCC 1488 Thr His Glu Phe Tyr Val Arg Lys Gly Gly Ala Arg Lys Arg Pro Ala 485 490 495 CCC AAT GAC GCA GAT ATA AGT GAG CCC AAG CGG GCC TGT CCG TCA GTT 1536 Pro Asn Asp Ala Asp Ile Ser Glu Pro Lys Arg Ala Cys Pro Ser Val 500 505 510 GCG CAG CCA TCG ACG TCA GAC GCG GAA GCT CCG GTG GAC TAC GCG GAC 1584 Ala Gln Pro Ser Thr Ser Asp Ala Glu Ala Pro Val Asp Tyr Ala Asp 515 520 525 AGG TAC CAA AAC AAA TGT TCT CGT CAC GTG GGT ATG AAT CTG ATG CTT 1632 Arg Tyr Gln Asn Lys Cys Ser Arg His Val Gly Met Asn Leu Met Leu 530 535 540 TTT CCC TGC CGG CAA TGC GAG AGA ATG AAT CAG AAT GTG GAC ATT TGC 1680 Phe Pro Cys Arg Gln Cys Glu Arg Met Asn Gln Asn Val Asp Ile Cys 545 550 555 560 TTC ACG CAC GGG GTC ATG GAC TGT GCC GAG TGC TTC CCC GTG TCA GAA 1728 Phe Thr His Gly Val Met Asp Cys Ala Glu Cys Phe Pro Val Ser Glu 565 570 575 TCT CAA CCC GTG TCT GTC GTC AGA AAG CGG ACG TAT CAG AAA CTG TGT 1776 Ser Gln Pro Val Ser Val Val Arg Lys Arg Thr Tyr Gln Lys Leu Cys 580 585 590 CCG ATT CAT CAC ATC ATG GGG AGG GCG CCC GAG GTG GCC TGC TCG GCC 1824 Pro Ile His His Ile Met Gly Arg Ala Pro Glu Val Ala Cys Ser Ala 595 600 605 TGC GAA CTG GCC AAT GTG GAC TTG GAT GAC TGT GAC ATG GAA CAA TAA 1872 Cys Glu Leu Ala Asn Val Asp Leu Asp Asp Cys Asp Met Glu Gln * 610 615 620 734 amino acids amino acid linear <Unknown> protein AAV4 capsid protein VP1 4 Met Thr Asp Gly Tyr Leu Pro Asp Trp Leu Glu Asp Asn Leu Ser Glu 1 5 10 15 Gly Val Arg Glu Trp Trp Ala Leu Gln Pro Gly Ala Pro Lys Pro Lys 20 25 30 Ala Asn Gln Gln His Gln Asp Asn Ala Arg Gly Leu Val Leu Pro Gly 35 40 45 Tyr Lys Tyr Leu Gly Pro Gly Asn Gly Leu Asp Lys Gly Glu Pro Val 50 55 60 Asn Ala Ala Asp Ala Ala Ala Leu Glu His Asp Lys Ala Tyr Asp Gln 65 70 75 80 Gln Leu Lys Ala Gly Asp Asn Pro Tyr Leu Lys Tyr Asn His Ala Asp 85 90 95 Ala Glu Phe Gln Gln Arg Leu Gln Gly Asp Thr Ser Phe Gly Gly Asn 100 105 110 Leu Gly Arg Ala Val Phe Gln Ala Lys Lys Arg Val Leu Glu Pro Leu 115 120 125 Gly Leu Val Glu Gln Ala Gly Glu Thr Ala Pro Gly Lys Lys Arg Pro 130 135 140 Leu Ile Glu Ser Pro Gln Gln Pro Asp Ser Ser Thr Gly Ile Gly Lys 145 150 155 160 Lys Gly Lys Gln Pro Ala Lys Lys Lys Leu Val Phe Glu Asp Glu Thr 165 170 175 Gly Ala Gly Asp Gly Pro Pro Glu Gly Ser Thr Ser Gly Ala Met Ser 180 185 190 Asp Asp Ser Glu Met Arg Ala Ala Ala Gly Gly Ala Ala Val Glu Gly 195 200 205 Gly Gln Gly Ala Asp Gly Val Gly Asn Ala Ser Gly Asp Trp His Cys 210 215 220 Asp Ser Thr Trp Ser Glu Gly His Val Thr Thr Thr Ser Thr Arg Thr 225 230 235 240 Trp Val Leu Pro Thr Tyr Asn Asn His Leu Tyr Lys Arg Leu Gly Glu 245 250 255 Ser Leu Gln Ser Asn Thr Tyr Asn Gly Phe Ser Thr Pro Trp Gly Tyr 260 265 270 Phe Asp Phe Asn Arg Phe His Cys His Phe Ser Pro Arg Asp Trp Gln 275 280 285 Arg Leu Ile Asn Asn Asn Trp Gly Met Arg Pro Lys Ala Met Arg Val 290 295 300 Lys Ile Phe Asn Ile Gln Val Lys Glu Val Thr Thr Ser Asn Gly Glu 305 310 315 320 Thr Thr Val Ala Asn Asn Leu Thr Ser Thr Val Gln Ile Phe Ala Asp 325 330 335 Ser Ser Tyr Glu Leu Pro Tyr Val Met Asp Ala Gly Gln Glu Gly Ser 340 345 350 Leu Pro Pro Phe Pro Asn Asp Val Phe Met Val Pro Gln Tyr Gly Tyr 355 360 365 Cys Gly Leu Val Thr Gly Asn Thr Ser Gln Gln Gln Thr Asp Arg Asn 370 375 380 Ala Phe Tyr Cys Leu Glu Tyr Phe Pro Ser Gln Met Leu Arg Thr Gly 385 390 395 400 Asn Asn Phe Glu Ile Thr Tyr Ser Phe Glu Lys Val Pro Phe His Ser 405 410 415 Met Tyr Ala His Ser Gln Ser Leu Asp Arg Leu Met Asn Pro Leu Ile 420 425 430 Asp Gln Tyr Leu Trp Gly Leu Gln Ser Thr Thr Thr Gly Thr Thr Leu 435 440 445 Asn Ala Gly Thr Ala Thr Thr Asn Phe Thr Lys Leu Arg Pro Thr Asn 450 455 460 Phe Ser Asn Phe Lys Lys Asn Trp Leu Pro Gly Pro Ser Ile Lys Gln 465 470 475 480 Gln Gly Phe Ser Lys Thr Ala Asn Gln Asn Tyr Lys Ile Pro Ala Thr 485 490 495 Gly Ser Asp Ser Leu Ile Lys Tyr Glu Thr His Ser Thr Leu Asp Gly 500 505 510 Arg Trp Ser Ala Leu Thr Pro Gly Pro Pro Met Ala Thr Ala Gly Pro 515 520 525 Ala Asp Ser Lys Phe Ser Asn Ser Gln Leu Ile Phe Ala Gly Pro Lys 530 535 540 Gln Asn Gly Asn Thr Ala Thr Val Pro Gly Thr Leu Ile Phe Thr Ser 545 550 555 560 Glu Glu Glu Leu Ala Ala Thr Asn Ala Thr Asp Thr Asp Met Trp Gly 565 570 575 Asn Leu Pro Gly Gly Asp Gln Ser Asn Ser Asn Leu Pro Thr Val Asp 580 585 590 Arg Leu Thr Ala Leu Gly Ala Val Pro Gly Met Val Trp Gln Asn Arg 595 600 605 Asp Ile Tyr Tyr Gln Gly Pro Ile Trp Ala Lys Ile Pro His Thr Asp 610 615 620 Gly His Phe His Pro Ser Pro Leu Ile Gly Gly Phe Gly Leu Lys His 625 630 635 640 Pro Pro Pro Gln Ile Phe Ile Lys Asn Thr Pro Val Pro Ala Asn Pro 645 650 655 Ala Thr Thr Phe Ser Ser Thr Pro Val Asn Ser Phe Ile Thr Gln Tyr 660 665 670 Ser Thr Gly Gln Val Ser Val Gln Ile Asp Trp Glu Ile Gln Lys Glu 675 680 685 Arg Ser Lys Arg Trp Asn Pro Glu Val Gln Phe Thr Ser Asn Tyr Gly 690 695 700 Gln Gln Asn Ser Leu Leu Trp Ala Pro Asp Ala Ala Gly Lys Tyr Thr 705 710 715 720 Glu Pro Arg Ala Ile Gly Thr Arg Tyr Leu Thr His His Leu 725 730 2208 base pairs nucleic acid double linear AAV4 capsid protein VP1 gene 5 ATGACTGACG GTTACCTTCC AGATTGGCTA GAGGACAACC TCTCTGAAGG CGTTCGAGAC 60 TGGTGGGCGC TGCAACCTGG AGCCCCTAAA CCCAAGGCAA ATCAACAACA TCAGGACAAC 120 GCTCGGGGTC TTGTGCTTCC GGGTTACAAA TACCTCGGAC CCGGCAACGG ACTCGACAAG 180 GGGGAACCCG TCAACGCAGC GGACGCGGCA GCCCTCGAGC ACGACAAGGC CTACGACCAG 240 CAGCTCAAGG CCGGTGACAA CCCCTACCTC AAGTACAACC ACGCCGACGC GGAGTTCCAG 300 CAGCGGCTTC AGGGCGACAC ATCGTTTGGG GGCAACCTCG GCAGAGCAGT CTTCCAGGCC 360 AAAAAGAGGG TTCTTGAACC TCTTGGTCTG GTTGAGCAAG CGGGTGAGAC GGCTCCTGGA 420 AAGAAGAGAC CGTTGATTGA ATCCCCCCAG CAGCCCGACT CCTCCACGGG TATCGGCAAA 480 AAAGGCAAGC AGCCGGCTAA AAAGAAGCTC GTTTTCGAAG ACGAAACTGG AGCAGGCGAC 540 GGACCCCCTG AGGGATCAAC TTCCGGAGCC ATGTCTGATG ACAGTGAGAT GCGTGCAGGA 600 GCTGGCGGAG CTGCAGTCGA GGGSGGACAA GGTGCCGATG GAGTGGGTAA TGCCTCGGGT 660 GATTGGCATT GCGATTCCAC CTGGTCTGAG GGCCACGTCA CGACCACCAG CACCAGAACC 720 TGGGTCTTGC CCACCTACAA CAACCACCTN TACAAGCGAC TCGGAGAGAG CCTGCAGTCC 780 AACACCTACA ACGGATTCTC CACCCCCTGG GGATACTTTG ACTTCAACCG CTTCCACTGC 840 CACTTCTCAC CACGTGACTG GCAGCGACTC ATCAACAACA ACTGGGGCAT GCGACCCAAA 900 GCCATGCGGG TCAAAATCTT CAACATCCAG GTCAAGGAGG TCACGACGTC GAACGGCGAG 960 ACAACGGTGG CTAATAACCT TACCAGCACG GTTCAGATCT TTGCGGACTC GTCGTACGAA 1020 CTGCCGTACG TGATGGATGC GGGTCAAGAG GGCAGCCTGC CTCCTTTTCC CAACGACGTC 1080 TTTATGGTGC CCCAGTACGG CTACTGTGGA CTGGTGACCG GCAACACTTC GCAGCAACAG 1140 ACTGACAGAA ATGCCTTCTA CTGCCTGGAG TACTTTCCTT CGCAGATGCT GCGGACTGGC 1200 AACAACTTTG AAATTACGTA CAGTTTTGAG AAGGTGCCTT TCCACTCGAT GTACGCGCAC 1260 AGCCAGAGCC TGGACCGGCT GATGAACCCT CTCATCGACC AGTACCTGTG GGGACTGCAA 1320 TCGACCACCA CCGGAACCAC CCTGAATGCC GGGACTGCCA CCACCAACTT TACCAAGCTG 1380 CGGCCTACCA ACTTTTCCAA CTTTAAAAAG AACTGGCTGC CCGGGCCTTC AATCAAGCAG 1440 CAGGGCTTCT CAAAGACTGC CAATCAAAAC TACAAGATCC CTGCCACCGG GTCAGACAGT 1500 CTCATCAAAT ACGAGACGCA CAGCACTCTG GACGGAAGAT GGAGTGCCCT GACCCCCGCA 1560 CCTCCAATGG CCACGGCTGG ACCTGCGGAC AGCAAGTTCA GCAACAGCCA GCTCATCTTT 1620 GCGGGGCCTA AACAGAACGG CAACACGGCC ACCGTACCCG GGACTCTGAT CTTCACCTCT 1680 GAGGAGGAGC TGGCAGCCAC CAACGCCACC GATACGGACA TGTGGGGCAA CCTACCTGGC 1740 GGTGACCAGA GCAACAGCAA CCTGCCGACC GTGGACAGAC TGACAGCCTT GGGAGCCGTG 1800 CCTGGAATGG TCTGGCAAAA CAGAGACATT TACTACCAGG GTCCCATTTG GGCCAAGATT 1860 CCTCATACCG ATGGACACTT TCACCCCTCA CCGCTGATTG GTGGGTTTGG GCTGAAACAC 1920 CCGCCTCCTC AAATTTTTAT CAAGAACACC CCGGTACCTG CGAATCCTGC AACGACCTTC 1980 AGCTCTACTC CGGTAAACTC CTTCATTACT CAGTACAGCA CTGGCCAGGT GTCGGTGCAG 2040 ATTGACTGGG AGATCCAGAA GGAGCGGTCC AAACGCTGGA ACCCCGAGGT CCAGTTTACC 2100 TCCAACTACG GACAGCAAAA CTCTCTGTTG TGGGCTCCCG ATGCGGCTGG GAAATACACT 2160 GAGCCTAGGG CTATCGGTAC CCGCTACCTC ACCCACCACC TGTAATAA 2208 125 base pairs nucleic acid single linear AAV4 ITR “flip” orientation 6 TTGGCCACTC CCTCTATGCG CGCTCGCTCA CTCACTCGGC CCTGGAGACC AAAGGTCTCC 60 AGACTGCCGG CCTCTGGCCG GCAGGGCCGA GTGAGTGAGC GAGCGCGCAT AGAGGGAGTG 120 GCCAA 125 245 base pairs nucleic acid double linear AAV4 p5 promoter 7 CTCCATCATC TAGGTTTGCC CACTGACGTC AATGTGACGT CCTAGGGTTA GGGAGGTCCC 60 TGTATTAGCA GTCACGTGAG TGTCGTATTT CGCGGAGCGT AGCGGAGCGC ATACCAAGCT 120 GCCACGTCAC AGCCACGTGG TCCGTTTGCG ACAGTTTGCG ACACCATGTG GTCAGGAGGG 180 TATATAACCG CGAGTGAGCC AGCGAGGAGC TCCATTTTGC CCGCGAATTT TGAACGAGCA 240 GCAGC 245 313 amino acids amino acid linear <Unknown> protein AAV4 Rep protein 40 8 Met Glu Leu Val Gly Trp Leu Val Asp Arg Gly Ile Thr Ser Glu Lys 1 5 10 15 Gln Trp Ile Gln Glu Asp Gln Ala Ser Tyr Ile Ser Phe Asn Ala Ala 20 25 30 Ser Asn Ser Arg Ser Gln Ile Lys Ala Ala Leu Asp Asn Ala Ser Lys 35 40 45 Ile Met Ser Leu Thr Lys Thr Ala Pro Asp Tyr Leu Val Gly Gln Asn 50 55 60 Pro Pro Glu Asp Ile Ser Ser Asn Arg Ile Tyr Arg Ile Leu Glu Met 65 70 75 80 Asn Gly Tyr Asp Pro Gln Tyr Ala Ala Ser Val Phe Leu Gly Trp Ala 85 90 95 Gln Lys Lys Phe Gly Lys Arg Asn Thr Ile Trp Leu Phe Gly Pro Ala 100 105 110 Thr Thr Gly Lys Thr Asn Ile Ala Glu Ala Ile Ala His Ala Val Pro 115 120 125 Phe Tyr Gly Cys Val Asn Trp Thr Asn Glu Asn Phe Pro Phe Asn Asp 130 135 140 Cys Val Asp Lys Met Val Ile Trp Trp Glu Glu Gly Lys Met Thr Ala 145 150 155 160 Lys Val Val Glu Ser Ala Lys Ala Ile Leu Gly Gly Ser Lys Val Arg 165 170 175 Val Asp Gln Lys Cys Lys Ser Ser Ala Gln Ile Asp Pro Thr Pro Val 180 185 190 Ile Val Thr Ser Asn Thr Asn Met Cys Ala Val Ile Asp Gly Asn Ser 195 200 205 Thr Thr Phe Glu His Gln Gln Pro Leu Gln Asp Arg Met Phe Lys Phe 210 215 220 Glu Leu Thr Lys Arg Leu Glu His Asp Phe Gly Lys Val Thr Lys Gln 225 230 235 240 Glu Val Lys Asp Phe Phe Arg Trp Ala Ser Asp His Val Thr Glu Val 245 250 255 Thr His Glu Phe Tyr Val Arg Lys Gly Gly Ala Arg Lys Arg Pro Ala 260 265 270 Pro Asn Asp Ala Asp Ile Ser Glu Pro Lys Arg Ala Cys Pro Ser Val 275 280 285 Ala Gln Pro Ser Thr Ser Asp Ala Glu Ala Pro Val Asp Tyr Ala Asp 290 295 300 Arg Leu Ala Arg Gly Gln Pro Leu Xaa 305 310 399 amino acids amino acid linear <Unknown> protein AAV4 Rep protein 52 9 Met Glu Leu Val Gly Trp Leu Val Asp Arg Gly Ile Thr Ser Glu Lys 1 5 10 15 Gln Trp Ile Gln Glu Asp Gln Ala Ser Tyr Ile Ser Phe Asn Ala Ala 20 25 30 Ser Asn Ser Arg Ser Gln Ile Lys Ala Ala Leu Asp Asn Ala Ser Lys 35 40 45 Ile Met Ser Leu Thr Lys Thr Ala Pro Asp Tyr Leu Val Gly Gln Asn 50 55 60 Pro Pro Glu Asp Ile Ser Ser Asn Arg Ile Tyr Arg Ile Leu Glu Met 65 70 75 80 Asn Gly Tyr Asp Pro Gln Tyr Ala Ala Ser Val Phe Leu Gly Trp Ala 85 90 95 Gln Lys Lys Phe Gly Lys Arg Asn Thr Ile Trp Leu Phe Gly Pro Ala 100 105 110 Thr Thr Gly Lys Thr Asn Ile Ala Glu Ala Ile Ala His Ala Val Pro 115 120 125 Phe Tyr Gly Cys Val Asn Trp Thr Asn Glu Asn Phe Pro Phe Asn Asp 130 135 140 Cys Val Asp Lys Met Val Ile Trp Trp Glu Glu Gly Lys Met Thr Ala 145 150 155 160 Lys Val Val Glu Ser Ala Lys Ala Ile Leu Gly Gly Ser Lys Val Arg 165 170 175 Val Asp Gln Lys Cys Lys Ser Ser Ala Gln Ile Asp Pro Thr Pro Val 180 185 190 Ile Val Thr Ser Asn Thr Asn Met Cys Ala Val Ile Asp Gly Asn Ser 195 200 205 Thr Thr Phe Glu His Gln Gln Pro Leu Gln Asp Arg Met Phe Lys Phe 210 215 220 Glu Leu Thr Lys Arg Leu Glu His Asp Phe Gly Lys Val Thr Lys Gln 225 230 235 240 Glu Val Lys Asp Phe Phe Arg Trp Ala Ser Asp His Val Thr Glu Val 245 250 255 Thr His Glu Phe Tyr Val Arg Lys Gly Gly Ala Arg Lys Arg Pro Ala 260 265 270 Pro Asn Asp Ala Asp Ile Ser Glu Pro Lys Arg Ala Cys Pro Ser Val 275 280 285 Ala Gln Pro Ser Thr Ser Asp Ala Glu Ala Pro Val Asp Tyr Ala Asp 290 295 300 Arg Tyr Gln Asn Lys Cys Ser Arg His Val Gly Met Asn Leu Met Leu 305 310 315 320 Phe Pro Cys Arg Gln Cys Glu Arg Met Asn Gln Asn Val Asp Ile Cys 325 330 335 Phe Thr His Gly Val Met Asp Cys Ala Glu Cys Phe Pro Val Ser Glu 340 345 350 Ser Gln Pro Val Ser Val Val Arg Lys Arg Thr Tyr Gln Lys Leu Cys 355 360 365 Pro Ile His His Ile Met Gly Arg Ala Pro Glu Val Ala Cys Ser Ala 370 375 380 Cys Glu Leu Ala Asn Val Asp Leu Asp Asp Cys Asp Met Glu Gln 385 390 395 537 amino acids amino acid linear <Unknown> protein AAV4 Rep protein 68 10 Met Pro Gly Phe Tyr Glu Ile Val Leu Lys Val Pro Ser Asp Leu Asp 1 5 10 15 Glu His Leu Pro Gly Ile Ser Asp Ser Phe Val Ser Trp Val Ala Glu 20 25 30 Lys Glu Trp Glu Leu Pro Pro Asp Ser Asp Met Asp Leu Asn Leu Ile 35 40 45 Glu Gln Ala Pro Leu Thr Val Ala Glu Lys Leu Gln Arg Glu Phe Leu 50 55 60 Val Glu Trp Arg Arg Val Ser Lys Ala Pro Glu Ala Leu Phe Phe Val 65 70 75 80 Gln Phe Glu Lys Gly Asp Ser Tyr Phe His Leu His Ile Leu Val Glu 85 90 95 Thr Val Gly Val Lys Ser Met Val Val Gly Arg Tyr Val Ser Gln Ile 100 105 110 Lys Glu Lys Leu Val Thr Arg Ile Tyr Arg Gly Val Glu Pro Gln Leu 115 120 125 Pro Asn Trp Phe Ala Val Thr Lys Thr Arg Asn Gly Ala Gly Gly Gly 130 135 140 Asn Lys Val Val Asp Asp Cys Tyr Ile Pro Asn Tyr Leu Leu Pro Lys 145 150 155 160 Thr Gln Pro Glu Leu Gln Trp Ala Trp Thr Asn Met Asp Gln Tyr Ile 165 170 175 Ser Ala Cys Leu Asn Leu Ala Glu Arg Lys Arg Leu Val Ala Gln His 180 185 190 Leu Thr His Val Ser Gln Thr Gln Glu Gln Asn Lys Glu Asn Gln Asn 195 200 205 Pro Asn Ser Asp Ala Pro Val Ile Arg Ser Lys Thr Ser Ala Arg Tyr 210 215 220 Met Glu Leu Val Gly Trp Leu Val Asp Arg Gly Ile Thr Ser Glu Lys 225 230 235 240 Gln Trp Ile Gln Glu Asp Gln Ala Ser Tyr Ile Ser Phe Asn Ala Ala 245 250 255 Ser Asn Ser Arg Ser Gln Ile Lys Ala Ala Leu Asp Asn Ala Ser Lys 260 265 270 Ile Met Ser Leu Thr Lys Thr Ala Pro Asp Tyr Leu Val Gly Gln Asn 275 280 285 Pro Pro Glu Asp Ile Ser Ser Asn Arg Ile Tyr Arg Ile Leu Glu Met 290 295 300 Asn Gly Tyr Asp Pro Gln Tyr Ala Ala Ser Val Phe Leu Gly Trp Ala 305 310 315 320 Gln Lys Lys Phe Gly Lys Arg Asn Thr Ile Trp Leu Phe Gly Pro Ala 325 330 335 Thr Thr Gly Lys Thr Asn Ile Ala Glu Ala Ile Ala His Ala Val Pro 340 345 350 Phe Tyr Gly Cys Val Asn Trp Thr Asn Glu Asn Phe Pro Phe Asn Asp 355 360 365 Cys Val Asp Lys Met Val Ile Trp Trp Glu Glu Gly Lys Met Thr Ala 370 375 380 Lys Val Val Glu Ser Ala Lys Ala Ile Leu Gly Gly Ser Lys Val Arg 385 390 395 400 Val Asp Gln Lys Cys Lys Ser Ser Ala Gln Ile Asp Pro Thr Pro Val 405 410 415 Ile Val Thr Ser Asn Thr Asn Met Cys Ala Val Ile Asp Gly Asn Ser 420 425 430 Thr Thr Phe Glu His Gln Gln Pro Leu Gln Asp Arg Met Phe Lys Phe 435 440 445 Glu Leu Thr Lys Arg Leu Glu His Asp Phe Gly Lys Val Thr Lys Gln 450 455 460 Glu Val Lys Asp Phe Phe Arg Trp Ala Ser Asp His Val Thr Glu Val 465 470 475 480 Thr His Glu Phe Tyr Val Arg Lys Gly Gly Ala Arg Lys Arg Pro Ala 485 490 495 Pro Asn Asp Ala Asp Ile Ser Glu Pro Lys Arg Ala Cys Pro Ser Val 500 505 510 Ala Gln Pro Ser Thr Ser Asp Ala Glu Ala Pro Val Asp Tyr Ala Asp 515 520 525 Arg Leu Ala Arg Gly Gln Pro Leu Xaa 530 535 623 amino acids amino acid linear <Unknown> protein AAV4 Rep protein 78 11 Met Pro Gly Phe Tyr Glu Ile Val Leu Lys Val Pro Ser Asp Leu Asp 1 5 10 15 Glu His Leu Pro Gly Ile Ser Asp Ser Phe Val Ser Trp Val Ala Glu 20 25 30 Lys Glu Trp Glu Leu Pro Pro Asp Ser Asp Met Asp Leu Asn Leu Ile 35 40 45 Glu Gln Ala Pro Leu Thr Val Ala Glu Lys Leu Gln Arg Glu Phe Leu 50 55 60 Val Glu Trp Arg Arg Val Ser Lys Ala Pro Glu Ala Leu Phe Phe Val 65 70 75 80 Gln Phe Glu Lys Gly Asp Ser Tyr Phe His Leu His Ile Leu Val Glu 85 90 95 Thr Val Gly Val Lys Ser Met Val Val Gly Arg Tyr Val Ser Gln Ile 100 105 110 Lys Glu Lys Leu Val Thr Arg Ile Tyr Arg Gly Val Glu Pro Gln Leu 115 120 125 Pro Asn Trp Phe Ala Val Thr Lys Thr Arg Asn Gly Ala Gly Gly Gly 130 135 140 Asn Lys Val Val Asp Asp Cys Tyr Ile Pro Asn Tyr Leu Leu Pro Lys 145 150 155 160 Thr Gln Pro Glu Leu Gln Trp Ala Trp Thr Asn Met Asp Gln Tyr Ile 165 170 175 Ser Ala Cys Leu Asn Leu Ala Glu Arg Lys Arg Leu Val Ala Gln His 180 185 190 Leu Thr His Val Ser Gln Thr Gln Glu Gln Asn Lys Glu Asn Gln Asn 195 200 205 Pro Asn Ser Asp Ala Pro Val Ile Arg Ser Lys Thr Ser Ala Arg Tyr 210 215 220 Met Glu Leu Val Gly Trp Leu Val Asp Arg Gly Ile Thr Ser Glu Lys 225 230 235 240 Gln Trp Ile Gln Glu Asp Gln Ala Ser Tyr Ile Ser Phe Asn Ala Ala 245 250 255 Ser Asn Ser Arg Ser Gln Ile Lys Ala Ala Leu Asp Asn Ala Ser Lys 260 265 270 Ile Met Ser Leu Thr Lys Thr Ala Pro Asp Tyr Leu Val Gly Gln Asn 275 280 285 Pro Pro Glu Asp Ile Ser Ser Asn Arg Ile Tyr Arg Ile Leu Glu Met 290 295 300 Asn Gly Tyr Asp Pro Gln Tyr Ala Ala Ser Val Phe Leu Gly Trp Ala 305 310 315 320 Gln Lys Lys Phe Gly Lys Arg Asn Thr Ile Trp Leu Phe Gly Pro Ala 325 330 335 Thr Thr Gly Lys Thr Asn Ile Ala Glu Ala Ile Ala His Ala Val Pro 340 345 350 Phe Tyr Gly Cys Val Asn Trp Thr Asn Glu Asn Phe Pro Phe Asn Asp 355 360 365 Cys Val Asp Lys Met Val Ile Trp Trp Glu Glu Gly Lys Met Thr Ala 370 375 380 Lys Val Val Glu Ser Ala Lys Ala Ile Leu Gly Gly Ser Lys Val Arg 385 390 395 400 Val Asp Gln Lys Cys Lys Ser Ser Ala Gln Ile Asp Pro Thr Pro Val 405 410 415 Ile Val Thr Ser Asn Thr Asn Met Cys Ala Val Ile Asp Gly Asn Ser 420 425 430 Thr Thr Phe Glu His Gln Gln Pro Leu Gln Asp Arg Met Phe Lys Phe 435 440 445 Glu Leu Thr Lys Arg Leu Glu His Asp Phe Gly Lys Val Thr Lys Gln 450 455 460 Glu Val Lys Asp Phe Phe Arg Trp Ala Ser Asp His Val Thr Glu Val 465 470 475 480 Thr His Glu Phe Tyr Val Arg Lys Gly Gly Ala Arg Lys Arg Pro Ala 485 490 495 Pro Asn Asp Ala Asp Ile Ser Glu Pro Lys Arg Ala Cys Pro Ser Val 500 505 510 Ala Gln Pro Ser Thr Ser Asp Ala Glu Ala Pro Val Asp Tyr Ala Asp 515 520 525 Arg Tyr Gln Asn Lys Cys Ser Arg His Val Gly Met Asn Leu Met Leu 530 535 540 Phe Pro Cys Arg Gln Cys Glu Arg Met Asn Gln Asn Val Asp Ile Cys 545 550 555 560 Phe Thr His Gly Val Met Asp Cys Ala Glu Cys Phe Pro Val Ser Glu 565 570 575 Ser Gln Pro Val Ser Val Val Arg Lys Arg Thr Tyr Gln Lys Leu Cys 580 585 590 Pro Ile His His Ile Met Gly Arg Ala Pro Glu Val Ala Cys Ser Ala 595 600 605 Cys Glu Leu Ala Asn Val Asp Leu Asp Asp Cys Asp Met Glu Gln 610 615 620 939 base pairs nucleic acid double linear AAV4 Rep 40 gene 12 ATGGAGCTGG TCGGGTGGCT GGTGGACCGC GGGATCACGT CAGAAAAGCA ATGGATCCAG 60 GAGGACCAGG CGTCCTACAT CTCCTTCAAC GCCGCCTCCA ACTCGCGGTC ACAAATCAAG 120 GCCGCGCTGG ACAATGCCTC CAAAATCATG AGCCTGACAA AGACGGCTCC GGACTACCTG 180 GTGGGCCAGA ACCCGCCGGA GGACATTTCC AGCAACCGCA TCTACCGAAT CCTCGAGATG 240 AACGGGTACG ATCCGCAGTA CGCGGCCTCC GTCTTCCTGG GCTGGGCGCA AAAGAAGTTC 300 GGGAAGAGGA ACACCATCTG GCTCTTTGGG CCGGCCACGA CGGGTAAAAC CAACATCGCG 360 GAAGCCATCG CCCACGCCGT GCCCTTCTAC GGCTGCGTGA ACTGGACCAA TGAGAACTTT 420 CCGTTCAACG ATTGCGTCGA CAAGATGGTG ATCTGGTGGG AGGAGGGCAA GATGACGGCC 480 AAGGTCGTAG AGAGCGCCAA GGCCATCCTG GGCGGAAGCA AGGTGCGCGT GGACCAAAAG 540 TGCAAGTCAT CGGCCCAGAT CGACCCAACT CCCGTGATCG TCACCTCCAA CACCAACATG 600 TGCGCGGTCA TCGACGGAAA CTCGACCACC TTCGAGCACC AACAACCACT CCAGGACCGC 660 ATGTTCAAGT TCGAGCTCAC CAAGCGCCTG GAGCACGACT TTGGCAAGGT CACCAAGCAG 720 GAAGTCAAAG ACTTTTTCCG GTGGGCGTCA GATCACGTGA CCGAGGTGAC TCACGAGTTT 780 TACGTCAGAA AGGGTGGAGC TAGAAAGAGG CCCGCCCCCA ATGACGCAGA TATAAGTGTT 840 CCCAAGCGGG CCTGTCCGTC AGTTGCGCAG CCATCGACGT CAGACGCGGA AGCTCCGGTG 900 GACTACGCGG ACAGATTGGC TAGAGGACAA CCTCTCTGA 939 1197 base pairs nucleic acid double linear AAV4 Rep 52 gene 13 ATGGAGCTGG TCGGGTGGCT GGTGGACCGC GGGATCACGT CAGAAAAGCA ATGGATCCAG 60 GAGGACCAGG CGTCCTACAT CTCCTTCAAC GCCGCCTCCA ACTCGCGGTC ACAAATCAAG 120 GCCGCGCTGG ACAATGCCTC CAAAATCATG AGCCTGACAA AGACGGCTCC GGACTACCTG 180 GTGGGCCAGA ACCCGCCGGA GGACATTTCC AGCAACCGCA TCTACCGAAT CCTCGAGATG 240 AACGGGTACG ATCCGCAGTA CGCGGCCTCC GTCTTCCTGG GCTGGGCGCA AAAGAAGTTC 300 GGGAAGAGGA ACACCATCTG GCTCTTTGGG CCGGCCACGA CGGGTAAAAC CAACATCGCG 360 GAAGCCATCG CCCACGCCGT GCCCTTCTAC GGCTGCGTGA ACTGGACCAA TGAGAACTTT 420 CCGTTCAACG ATTGCGTCGA CAAGATGGTG ATCTGGTGGG AGGAGGGCAA GATGACGGCC 480 AAGGTCGTAG AGAGCGCCAA GGCCATCCTG GGCGGAAGCA AGGTGCGCGT GGACCAAAAG 540 TGCAAGTCAT CGGCCCAGAT CGACCCAACT CCCGTGATCG TCACCTCCAA CACCAACATG 600 TGCGCGGTCA TCGACGGAAA CTCGACCACC TTCGAGCACC AACAACCACT CCAGGACCGG 660 ATGTTCAAGT TCGAGCTCAC CAAGCGCCTG GAGCACGACT TTGGCAAGGT CACCAAGCAG 720 GAAGTCAAAG ACTTTTTCCG GTGGGCGTCA GATCACGTGA CCGAGGTGAC TCACGAGTTT 780 TACGTCAGAA AGGGTGGAGC TAGAAAGAGG CCCGCCCCCA ATGACGCAGA TATAAGTGAG 840 CCCAAGCGGG CCTGTCCGTC AGTTGCGCAG CCATCGACGT CAGACGCGGA AGCTCCGGTG 900 GACTACGCGG ACAGGTACCA AAACAAATGT TCTCGTCACG TGGGTATGAA TCTGATGCTT 960 TTTCCCTGCC GGCAATGCGA GAGAATGAAT CAGAATGTGG ACATTTGCTT CACGCACGGG 1020 GTCATGGACT GTGCCGAGTG CTTCCCCGTG TCAGAATCTC AACCCGTGTC TGTCGTCAGA 1080 AAGCGGACGT ATCAGAAACT GTGTCCGATT CATCACATCA TGGGGAGGGC GCCCGAGGTC 1140 GCCTGCTCGG CCTGCGAACT GGCCAATGTG GACTTGGATG ACTGTGACAT GGAACAA 1197 1611 base pairs nucleic acid double linear AAV4 Rep 68 gene 14 ATGCCGGGGT TCTACGAGAT CGTGCTGAAG GTGCCCAGCG ACCTGGACGA GCACCTGCCC 60 GGCATTTCTG ACTCTTTTGT GAGCTGGGTG GCCGAGAAGG AATGGGAGCT GCCGCCGGAT 120 TCTGACATGG ACTTGAATCT GATTGAGCAG GCACCCCTGA CCGTGGCCGA AAAGCTGCAA 180 CGCGAGTTCC TGGTCGAGTG GCGCCGCGTG AGTAAGGCCC CGGAGGCCCT CTTCTTTGTC 240 CAGTTCGAGA AGGGGGACAG CTACTTCCAC CTGCACATCC TGGTGGAGAC CGTGGGCGTC 300 AAATCCATGG TGGTGGGCCG CTACGTGAGC CAGATTAAAG AGAAGCTGGT GACCCGCATC 360 TACCGCGGGG TCGAGCCGCA GCTTCCGAAC TGGTTCGCGG TGACCAAGAC GCGTAATGGC 420 GCCGGAGGCG GGAACAAGGT GGTGGACGAC TGCTACATCC CCAACTACCT GCTCCCCAAG 480 ACCCAGCCCG AGCTCCAGTG GGCGTGGACT AACATGGACC AGTATATAAG CGCCTGTTTG 540 AATCTCGCGG AGCGTAAACG GCTGGTGGCG CAGCATCTGA CGCACGTGTC GCAGACGCAG 600 GAGCAGAACA AGGAAAACCA GAACCCCAAT TCTGACGCGC CGGTCATCAG GTCAAAAACC 660 TCCGCCAGGT ACATGGAGCT GGTCGGGTGG CTGGTGGACC GCGGGATCAC GTCAGAAAAG 720 CAATGGATCC AGGAGGACCA GGCGTCCTAC ATCTCCTTCA ACGCCGCCTC CAACTCGCGG 780 TCACAAATCA AGGCCGCGCT GGACAATGCC TCCAAAATCA TGAGCCTGAC AAAGACGGCT 840 CCGGACTACC TGGTGGGCCA GAACCCGCCG GAGGACATTT CCAGCAACCG CATCTACCGA 900 ATCCTCGAGA TGAACGGGTA CGATCCGCAG TACGCGGCCT CCGTCTTCCT GGGCTGGGCG 960 CAAAAGAAGT TCGGGAAGAG GAACACCATC TGGCTCTTTG GGCCGGCCAC GACGGGTAAA 1020 ACCAACATCG CGGAAGCCAT CGCCCACGCC GTGCCCTTCT ACGGCTGCGT GAACTGGACC 1080 AATGAGAACT TTCCGTTCAA CGATTGCGTC GACAAGATGG TGATCTGGTG GGAGGAGGGC 1140 AAGATGACGG CCAAGGTCGT AGAGAGCGCC AAGGCCATCC TGGGCGGAAG CAAGGTGCGC 1200 GTGGACCAAA AGTGCAAGTC ATCGGCCCAG ATCGACCCAA CTCCCGTGAT CGTCACCTCC 1260 AACACCAACA TGTGCGCGGT CATCGACGGA AACTCGACCA CCTTCGAGCA CCAACAACCA 1320 CTCCAGGACC GGATGTTCAA GTTCGAGCTC ACCAAGCGCC TGGAGCACGA CTTTGGCAAG 1380 GTCACCAAGC AGGAAGTCAA AGACTTTTTC CGGTGGGCGT CAGATCACGT GACCGAGGTG 1440 ACTCACGAGT TTTACGTCAG AAAGGGTGGA GCTAGAAAGA GGCCCGCCCC CAATGACGCA 1500 GATATAAGTG AGCCCAAGCG GGCCTGTCCG TCAGTTGCGC AGCCATCGAC GTCAGACGCG 1560 GAAGCTCCGG TGGACTACGC GGACAGATTG GCTAGAGGAC AACCTCTCTG A 1611 1872 base pairs nucleic acid double linear AAV4 Rep 78 gene 15 ATGCCGGGGT TCTACGAGAT CGTGCTGAAG GTGCCCAGCG ACCTGGACGA GCACCTGCC 60 GGCATTTCTG ACTCTTTTGT GAGCTGGGTG GCCGAGAAGG AATGGGAGCT GCCGCCGG 120 TCTGACATGG ACTTGAATCT GATTGAGCAG GCACCCCTGA CCGTGGCCGA AAAGCTGC 180 CGCGAGTTCC TGGTCGAGTG GCGCCGCGTG AGTAAGGCCC CGGAGGCCCT CTTCTTTG 240 CAGTTCGAGA AGGGGGACAG CTACTTCCAC CTGCACATCC TGGTGGAGAC CGTGGGCG 300 AAATCCATGG TGGTGGGCCG CTACGTGAGC CAGATTAAAG AGAAGCTGGT GACCCGCA 360 TACCGCGGGG TCGAGCCGCA GCTTCCGAAC TGGTTCGCGG TGACCAAGAC GCGTAATG 420 GCCGGAGGCG GGAACAAGGT GGTGGACGAC TGCTACATCC CCAACTACCT GCTCCCCA 480 ACCCAGCCCG AGCTCCAGTG GGCGTGGACT AACATGGACC AGTATATAAG CGCCTGTT 540 AATCTCGCGG AGCGTAAACG GCTGGTGGCG CAGCATCTGA CGCACGTGTC GCAGACGC 600 GAGCAGAACA AGGAAAACCA GAACCCCAAT TCTGACGCGC CGGTCATCAG GTCAAAAA 660 TCCGCCAGGT ACATGGAGCT GGTCGGGTGG CTGGTGGACC GCGGGATCAC GTCAGAAA 720 CAATGGATCC AGGAGGACCA GGCGTCCTAC ATCTCCTTCA ACGCCGCCTC CAACTCGC 780 TCACAAATCA AGGCCGCGCT GGACAATGCC TCCAAAATCA TGAGCCTGAC AAAGACGG 840 CCGGACTACC TGGTGGGCCA GAACCCGCCG GAGGACATTT CCAGCAACCG CATCTACC 900 ATCCTCGAGA TGAACGGGTA CGATCCGCAG TACGCGGCCT CCGTCTTCCT GGGCTGGG 960 CAAAAGAAGT TCGGGAAGAG GAACACCATC TGGCTCTTTG GGCCGGCCAC GACGGGT 1020 ACCAACATCG CGGAAGCCAT CGCCCACGCC GTGCCCTTCT ACGGCTGCGT GAACTGG 1080 AATGAGAACT TTCCGTTCAA CGATTGCGTC GACAAGATGG TGATCTGGTG GGAGGAG 1140 AAGATGACGG CCAAGGTCGT AGAGAGCGCC AAGGCCATCC TGGGCGGAAG CAAGGTG 1200 GTGGACCAAA AGTGCAAGTC ATCGGCCCAG ATCGACCCAA CTCCCGTGAT CGTCACC 1260 AACACCAACA TGTGCGCGGT CATCGACGGA AACTCGACCA CCTTCGAGCA CCAACAA 1320 CTCCAGGACC GGATGTTCAA GTTCGAGCTC ACCAAGCGCC TGGAGCACGA CTTTGGC 1380 GTCACCAAGC AGGAAGTCAA AGACTTTTTC CGGTGGGCGT CAGATCACGT GACCGAG 1440 ACTCACGAGT TTTACGTCAG AAAGGGTGGA GCTAGAAAGA GGCCCGCCCC CAATGAC 1500 GATATAAGTG AGCCCAAGCG GGCCTGTCCG TCAGTTGCGC AGCCATCGAC GTCAGAC 1560 GAAGCTCCGG TGGACTACGC GGACAGGTAC CAAAACAAAT GTTCTCGTCA CGTGGGT 1620 AATCTGATGC TTTTTCCCTG CCGGCAATGC GAGAGAATGA ATCAGAATGT GGACATT 1680 TTCACGCACG GGGTCATGGA CTGTGCCGAG TGCTTCCCCG TGTCAGAATC TCAACCC 1740 TCTGTCGTCA GAAAGCGGAC GTATCAGAAA CTGTGTCCGA TTCATCACAT CATGGGG 1800 GCGCCCGAGG TGGCCTGCTC GGCCTGCGAA CTGGCCAATG TGGACTTGGA TGACTGT 1860 ATGGAACAAT AA 1872 598 amino acids amino acid linear <Unknown> protein AAV4 capsid protein VP2 16 Thr Ala Pro Gly Lys Lys Arg Pro Leu Ile Glu Ser Pro Gln Gln Pro 1 5 10 15 Asp Ser Ser Thr Gly Ile Gly Lys Lys Gly Lys Gln Pro Ala Lys Lys 20 25 30 Lys Leu Val Phe Glu Asp Glu Thr Gly Ala Gly Asp Gly Pro Pro Glu 35 40 45 Gly Ser Thr Ser Gly Ala Met Ser Asp Asp Ser Glu Met Arg Ala Ala 50 55 60 Ala Gly Gly Ala Ala Val Glu Gly Gly Gln Gly Ala Asp Gly Val Gly 65 70 75 80 Asn Ala Ser Gly Asp Trp His Cys Asp Ser Thr Trp Ser Glu Gly His 85 90 95 Val Thr Thr Thr Ser Thr Arg Thr Trp Val Leu Pro Thr Tyr Asn Asn 100 105 110 His Leu Tyr Lys Arg Leu Gly Glu Ser Leu Gln Ser Asn Thr Tyr Asn 115 120 125 Gly Phe Ser Thr Pro Trp Gly Tyr Phe Asp Phe Asn Arg Phe His Cys 130 135 140 His Phe Ser Pro Arg Asp Trp Gln Arg Leu Ile Asn Asn Asn Trp Gly 145 150 155 160 Met Arg Pro Lys Ala Met Arg Val Lys Ile Phe Asn Ile Gln Val Lys 165 170 175 Glu Val Thr Thr Ser Asn Gly Glu Thr Thr Val Ala Asn Asn Leu Thr 180 185 190 Ser Thr Val Gln Ile Phe Ala Asp Ser Ser Tyr Glu Leu Pro Tyr Val 195 200 205 Met Asp Ala Gly Gln Glu Gly Ser Leu Pro Pro Phe Pro Asn Asp Val 210 215 220 Phe Met Val Pro Gln Tyr Gly Tyr Cys Gly Leu Val Thr Gly Asn Thr 225 230 235 240 Ser Gln Gln Gln Thr Asp Arg Asn Ala Phe Tyr Cys Leu Glu Tyr Phe 245 250 255 Pro Ser Gln Met Leu Arg Thr Gly Asn Asn Phe Glu Ile Thr Tyr Ser 260 265 270 Phe Glu Lys Val Pro Phe His Ser Met Tyr Ala His Ser Gln Ser Leu 275 280 285 Asp Arg Leu Met Asn Pro Leu Ile Asp Gln Tyr Leu Trp Gly Leu Gln 290 295 300 Ser Thr Thr Thr Gly Thr Thr Leu Asn Ala Gly Thr Ala Thr Thr Asn 305 310 315 320 Phe Thr Lys Leu Arg Pro Thr Asn Phe Ser Asn Phe Lys Lys Asn Trp 325 330 335 Leu Pro Gly Pro Ser Ile Lys Gln Gln Gly Phe Ser Lys Thr Ala Asn 340 345 350 Gln Asn Tyr Lys Ile Pro Ala Thr Gly Ser Asp Ser Leu Ile Lys Tyr 355 360 365 Glu Thr His Ser Thr Leu Asp Gly Arg Trp Ser Ala Leu Thr Pro Gly 370 375 380 Pro Pro Met Ala Thr Ala Gly Pro Ala Asp Ser Lys Phe Ser Asn Ser 385 390 395 400 Gln Leu Ile Phe Ala Gly Pro Lys Gln Asn Gly Asn Thr Ala Thr Val 405 410 415 Pro Gly Thr Leu Ile Phe Thr Ser Glu Glu Glu Leu Ala Ala Thr Asn 420 425 430 Ala Thr Asp Thr Asp Met Trp Gly Asn Leu Pro Gly Gly Asp Gln Ser 435 440 445 Asn Ser Asn Leu Pro Thr Val Asp Arg Leu Thr Ala Leu Gly Ala Val 450 455 460 Pro Gly Met Val Trp Gln Asn Arg Asp Ile Tyr Tyr Gln Gly Pro Ile 465 470 475 480 Trp Ala Lys Ile Pro His Thr Asp Gly His Phe His Pro Ser Pro Leu 485 490 495 Ile Gly Gly Phe Gly Leu Lys His Pro Pro Pro Gln Ile Phe Ile Lys 500 505 510 Asn Thr Pro Val Pro Ala Asn Pro Ala Thr Thr Phe Ser Ser Thr Pro 515 520 525 Val Asn Ser Phe Ile Thr Gln Tyr Ser Thr Gly Gln Val Ser Val Gln 530 535 540 Ile Asp Trp Glu Ile Gln Lys Glu Arg Ser Lys Arg Trp Asn Pro Glu 545 550 555 560 Val Gln Phe Thr Ser Asn Tyr Gly Gln Gln Asn Ser Leu Leu Trp Ala 565 570 575 Pro Asp Ala Ala Gly Lys Tyr Thr Glu Pro Arg Ala Ile Gly Thr Arg 580 585 590 Tyr Leu Thr His His Leu 595 1800 base pairs nucleic acid double linear AAV4 capsid protein VP2 gene 17 ACGGCTCCTG GAAAGAAGAG ACCGTTGATT GAATCCCCCC AGCAGCCCGA CTCCTCCACG 60 GGTATCGGCA AAAAAGGCAA GCAGCCGGCT AAAAAGAAGC TCGTTTTCGA AGACGAAACT 120 GGAGCAGGCG ACGGACCCCC TGAGGGATCA ACTTCCGGAG CCATGTCTGA TGACAGTGAG 180 ATGCGTGCAG CAGCTGGCGG AGCTGCAGTC GAGGGSGGAC AAGGTGCCGA TGGAGTGGGT 240 AATGCCTCGG GTGATTGGCA TTGCGATTCC ACCTGGTCTG AGGGCCACGT CACGACCACC 300 AGCACCAGAA CCTGGGTCTT GCCCACCTAC AACAACCACC TNTACAAGCG ACTCGGAGAG 360 AGCCTGCAGT CCAACACCTA CAACGGATTC TCCACCCCCT GGGGATACTT TGACTTCAAC 420 CGCTTCCACT GCCACTTCTC ACCACGTGAC TGGCAGCGAC TCATCAACAA CAACTGGGGC 480 ATGCGACCCA AAGCCATGCG GGTCAAAATC TTCAACATCC AGGTCAAGGA GGTCACGACG 540 TCGAACGGCG AGACAACGGT GGCTAATAAC CTTACCAGCA CGGTTCAGAT CTTTGCGGAC 600 TCGTCGTACG AACTGCCGTA CGTGATGGAT GCGGGTCAAG AGGGCAGCCT GCCTCCTTTT 660 CCCAACGACG TCTTTATGGT GCCCCAGTAC GGCTACTGTG GACTGGTGAC CGGCAACACT 720 TCGCAGCAAC AGACTGACAG AAATGCCTTC TACTGCCTGG AGTACTTTCC TTCGCAGATG 780 CTGCGGACTG GCAACAACTT TGAAATTACG TACAGTTTTG AGAAGGTGCC TTTCCACTCG 840 ATGTACGCGC ACAGCCAGAG CCTGGACCGG CTGATGAACC CTCTCATCGA CCAGTACCTG 900 TGGGGACTGC AATCGACCAC CACCGGAACC ACCCTGAATG CCGGGACTGC CACCACCAAC 960 TTTACCAAGC TGCGGCCTAC CAACTTTTCC AACTTTAAAA AGAACTGGCT GCCCGGGCCT 1020 TCAATCAAGC AGCAGGGCTT CTCAAAGACT GCCAATCAAA ACTACAAGAT CCCTGCCACC 1080 GGGTCAGACA GTCTCATCAA ATACGAGACG CACAGCACTC TGGACGGAAG ATGGAGTGCC 1140 CTGACCCCCG GACCTCCAAT GGCCACGGCT GGACCTGCGG ACAGCAAGTT CAGCAACAGC 1200 CAGCTCATCT TTGCGGGGCC TAAACAGAAC GGCAACACGG CCACCGTACC CGGGACTCTG 1260 ATCTTCACCT CTGAGGAGGA GCTGGCAGCC ACCAACGCCA CCGATACGGA CATGTGGGGC 1320 AACCTACCTG GCGGTGACCA GAGCAACAGC AACCTGCCGA CCGTGGACAG ACTGACAGCC 1380 TTGGGAGCCG TGCCTGGAAT GGTCTGGCAA AACAGAGACA TTTACTACCA GGGTCCCATT 1440 TGGGCCAAGA TTCCTCATAC CGATGGACAC TTTCACCCCT CACCGCTGAT TGGTGGGTTT 1500 GGGCTGAAAC ACCCGCCTCC TCAAATTTTT ATCAAGAACA CCCCGGTACC TGCGAATCCT 1560 GCAACGACCT TCAGCTCTAC TCCGGTAAAC TCCTTCATTA CTCAGTACAG CACTGGCCAG 1620 GTGTCGGTGC AGATTGACTG GGAGATCCAG AAGGAGCGGT CCAAACGCTG GAACCCCGCT 1680 GTCCAGTTTA CCTCCAACTA CGGACAGCAA AACTCTCTGT TGTGGGCTCC CGATGCGGCT 1740 GGGAAATACA CTGAGCCTAG GGCTATCGGT ACCCGCTACC TCACCCACCA CCTGTAATAA 1800 544 amino acids amino acid linear <Unknown> protein AAV4 capsid protein VP3 18 Met Ser Asp Asp Ser Glu Met Arg Ala Ala Ala Gly Gly Ala Ala Val 1 5 10 15 Glu Gly Gly Gln Gly Ala Asp Gly Val Gly Asn Ala Ser Gly Asp Trp 20 25 30 His Cys Asp Ser Thr Trp Ser Glu Gly His Val Thr Thr Thr Ser Thr 35 40 45 Arg Thr Trp Val Leu Pro Thr Tyr Asn Asn His Leu Tyr Lys Arg Leu 50 55 60 Gly Glu Ser Leu Gln Ser Asn Thr Tyr Asn Gly Phe Ser Thr Pro Trp 65 70 75 80 Gly Tyr Phe Asp Phe Asn Arg Phe His Cys His Phe Ser Pro Arg Asp 85 90 95 Trp Gln Arg Leu Ile Asn Asn Asn Trp Gly Met Arg Pro Lys Ala Met 100 105 110 Arg Val Lys Ile Phe Asn Ile Gln Val Lys Glu Val Thr Thr Ser Asn 115 120 125 Gly Glu Thr Thr Val Ala Asn Asn Leu Thr Ser Thr Val Gln Ile Phe 130 135 140 Ala Asp Ser Ser Tyr Glu Leu Pro Tyr Val Met Asp Ala Gly Gln Glu 145 150 155 160 Gly Ser Leu Pro Pro Phe Pro Asn Asp Val Phe Met Val Pro Gln Tyr 165 170 175 Gly Tyr Cys Gly Leu Val Thr Gly Asn Thr Ser Gln Gln Gln Thr Asp 180 185 190 Arg Asn Ala Phe Tyr Cys Leu Glu Tyr Phe Pro Ser Gln Met Leu Arg 195 200 205 Thr Gly Asn Asn Phe Glu Ile Thr Tyr Ser Phe Glu Lys Val Pro Phe 210 215 220 His Ser Met Tyr Ala His Ser Gln Ser Leu Asp Arg Leu Met Asn Pro 225 230 235 240 Leu Ile Asp Gln Tyr Leu Trp Gly Leu Gln Ser Thr Thr Thr Gly Thr 245 250 255 Thr Leu Asn Ala Gly Thr Ala Thr Thr Asn Phe Thr Lys Leu Arg Pro 260 265 270 Thr Asn Phe Ser Asn Phe Lys Lys Asn Trp Leu Pro Gly Pro Ser Ile 275 280 285 Lys Gln Gln Gly Phe Ser Lys Thr Ala Asn Gln Asn Tyr Lys Ile Pro 290 295 300 Ala Thr Gly Ser Asp Ser Leu Ile Lys Tyr Glu Thr His Ser Thr Leu 305 310 315 320 Asp Gly Arg Trp Ser Ala Leu Thr Pro Gly Pro Pro Met Ala Thr Ala 325 330 335 Gly Pro Ala Asp Ser Lys Phe Ser Asn Ser Gln Leu Ile Phe Ala Gly 340 345 350 Pro Lys Gln Asn Gly Asn Thr Ala Thr Val Pro Gly Thr Leu Ile Phe 355 360 365 Thr Ser Glu Glu Glu Leu Ala Ala Thr Asn Ala Thr Asp Thr Asp Met 370 375 380 Trp Gly Asn Leu Pro Gly Gly Asp Gln Ser Asn Ser Asn Leu Pro Thr 385 390 395 400 Val Asp Arg Leu Thr Ala Leu Gly Ala Val Pro Gly Met Val Trp Gln 405 410 415 Asn Arg Asp Ile Tyr Tyr Gln Gly Pro Ile Trp Ala Lys Ile Pro His 420 425 430 Thr Asp Gly His Phe His Pro Ser Pro Leu Ile Gly Gly Phe Gly Leu 435 440 445 Lys His Pro Pro Pro Gln Ile Phe Ile Lys Asn Thr Pro Val Pro Ala 450 455 460 Asn Pro Ala Thr Thr Phe Ser Ser Thr Pro Val Asn Ser Phe Ile Thr 465 470 475 480 Gln Tyr Ser Thr Gly Gln Val Ser Val Gln Ile Asp Trp Glu Ile Gln 485 490 495 Lys Glu Arg Ser Lys Arg Trp Asn Pro Glu Val Gln Phe Thr Ser Asn 500 505 510 Tyr Gly Gln Gln Asn Ser Leu Leu Trp Ala Pro Asp Ala Ala Gly Lys 515 520 525 Tyr Thr Glu Pro Arg Ala Ile Gly Thr Arg Tyr Leu Thr His His Leu 530 535 540 1617 base pairs nucleic acid double linear AAV4 capsid protein VP3 gene 19 ATGCGTGCAG CAGCTGGCGG AGCTGCAGTC GAGGGSGGAC AAGGTGCCGA TGGAGTGGGT 60 AATGCCTCGG GTGATTGGCA TTGCGATTCC ACCTGGTCTG AGGGCCACGT CACGACCACC 120 AGCACCAGAA CCTGGGTCTT GCCCACCTAC AACAACCACC TNTACAAGCG ACTCGGAGAG 180 AGCCTGCAGT CCAACACCTA CAACGGATTC TCCACCCCCT GGGGATACTT TGACTTCAAC 240 CGCTTCCACT GCCACTTCTC ACCACGTGAC TGGCAGCGAC TCATCAACAA CAACTGGGGC 300 ATGCGACCCA AAGCCATGCG GGTCAAAATC TTCAACATCC AGGTCAAGGA GGTCACGACG 360 TCGAACGGCG AGACAACGGT GGCTAATAAC CTTACCAGCA CGGTTCAGAT CTTTGCGGAC 420 TCGTCGTACG AACTGCCGTA CGTGATGGAT GCGGGTCAAG AGGGCAGCCT GCCTCCTTTT 480 CCCAACGACG TCTTTATGGT GCCCCAGTAC GGCTACTGTG GACTGGTGAC CGGCAACACT 540 TCGCAGCAAC AGACTGACAG AAATGCCTTC TACTGCCTGG AGTACTTTCC TTCGCAGATG 600 CTGCGGACTG GCAACAACTT TGAAATTACG TACAGTTTTG AGAAGGTGCC TTTCCACTCG 660 ATGTACGCGC ACAGCCAGAG CCTGGACCGG CTGATGAACC CTCTCATCGA CCAGTACCTG 720 TGGGGACTGC AATCGACCAC CACCGGAACC ACCCTGAATG CCGGGACTGC CACCACCAAC 780 TTTACCAAGC TGCGGCCTAC CAACTTTTCC AACTTTAAAA AGAACTGGCT GCCCGGGCCT 840 TCAATCAAGC AGCAGGGCTT CTCAAAGACT GCCAATCAAA ACTACAAGAT CCCTGCCACC 900 GGGTCAGACA GTCTCATCAA ATACGAGACG CACAGCACTC TGGACGGAAG ATGGAGTGCC 960 CTGACCCCCG GACCTCCAAT GGCCACGGCT GGACCTGCGG ACAGCAAGTT CAGCAACAGC 1020 CAGCTCATCT TTGCGGGGCC TAAACAGAAC GGCAACACGG CCACCGTACC CGGGACTCTG 1080 ATCTTCACCT CTGAGGAGGA GCTGGCAGCC ACCAACGCCA CCGATACGGA CATGTGGGGC 1140 AACCTACCTG GCGGTGACCA GAGCAACAGC AACCTGCCGA CCGTGGACAG ACTGACAGCC 1200 TTGGGAGCCG TGCCTGGAAT GGTCTGGCAA AACAGAGACA TTTACTACCA GGGTCCCATT 1260 TGGGCCAAGA TTCCTCATAC CGATGGACAC TTTCACCCCT CACCGCTGAT TGGTGGGTTT 1320 GGGCTGAAAC ACCCGCCTCC TCAAATTTTT ATCAAGAACA CCCCGGTACC TGCGAATCCT 1380 GCAACGACCT TCAGCTCTAC TCCGGTAAAC TCCTTCATTA CTCAGTACAG CACTGGCCAG 1440 GTGTCGGTGC AGATTGACTG GGAGATCCAG AAGGAGCGGT CCAAACGCTG GAACCCCGAG 1500 GTCCAGTTTA CCTCCAACTA CGGACAGCAA AACTCTCTGT TGTGGGCTCC CGATGCGGCT 1560 GGGAAATACA CTGAGCCTAG GGCTATCGGT ACCCGCTACC TCACCCACCA CCTGTAA 1617 129 base pairs nucleic acid single linear AAV4 ITR “flop” orientation 20 TTGGCCACTC CCTCTATGCG CGCTCGCTCA CTCACTCGGC CCTGCGGCCA GAGGCCGGCA 60 GTCTGGAGAC CTTTGGTGTC CAGGGCAGGG CCGAGTGAGT GAGCGAGCGC GCATAGAGGG 120 AGTGGCCAA 129 35 base pairs nucleic acid single linear 21 TCTAGTCTAG ACTTGGCCAC TCCCTCTCTG CGCGC 35 34 base pairs nucleic acid single linear 22 AGGCCTTAAG AGCAGTCGTC CACCACCTTG TTCC 34 

What is claimed is:
 1. A vector system for producing infectious virus particles having a characteristic of AAV4 comprising: at least one vector comprising a nucleic acid encoding an AAV4 capsid protein.
 2. The vector system of claim 1 comprising two vectors.
 3. The vector system of claim 2, wherein the first vector comprises a nucleic acid encoding an AAV4 capsid protein and the second vector comprises a pair of AAV inverted terminal repeats.
 4. The vector system of claim 2, wherein the first vector comprises a nucleic acid encoding an AAV4 Rep protein and the second vector comprises a pair of AAV inverted terminal repeats.
 5. The vector system of claim 2, wherein the first vector comprises a nucleic acid encoding an AAV4 Rep protein and a nucleic acid encoding an AAV4 capsid protein and the second vector comprises a pair of AAV inverted terminal repeats.
 6. The vector system according to claim 3, wherein the second vector comprises a pair of AAV2 inverted terminal repeats
 7. The vector system according to claim 3, wherein the second vector comprises a pair of AAV3 inverted terminal repeats.
 8. The vector system according to claim 3, wherein the second vector comprises a pair of AAV4 inverted terminal repeats.
 9. The vector system according to claim 8, wherein the AAV4 inverted terminal repeats comprise a Rep protein binding site having four “GAGC” repeats, wherein in the fourth nucleotide in the first two “GAGC” repeats is a T rather than a C.
 10. The vector system according to claim 9, wherein the AAV4 inverted terminal repeats comprise the nucleotide sequence set forth in SEQ ID NO:6.
 11. The vector system according to claim 9, wherein the AAV4 inverted terminal repeats comprise the nucleotide sequence set forth in SEQ ID NO:20.
 12. The vector system according to claim 3, wherein the second vector comprises a pair of AAV5 inverted terminal repeats.
 13. The vector system of claim 3, wherein the first vector further comprises a nucleic acid encoding an AAV2 Rep protein.
 14. The vector system of claim 3, wherein the first vector further comprises a nucleic acid encoding an AAV3 Rep protein.
 15. The vector system of claim 3, wherein the first vector further comprises a nucleic acid encoding an AAV4 Rep protein.
 16. The vector system of claim 15, wherein the adeno-associated virus 4 Rep protein has the amino acid sequence set forth in SEQ ID NO:2.
 17. The vector system of claim 15, wherein the adeno-associated virus 4 Rep protein has about 95% homology with the amino acid sequence set forth in SEQ ID NO:2.
 18. The vector system of claim 15, wherein the adeno-associated virus 4 Rep protein has the amino acid sequence set forth in SEQ ID NO:8.
 19. The vector system of claim 15, wherein the adeno-associated virus 4 Rep protein has about 95% homology with the amino acid sequence set forth in SEQ ID NO:8.
 20. The vector system of claim 15, wherein the adeno-associated virus 4 Rep protein has the amino acid sequence set forth in SEQ ID NO:9.
 21. The vector system of claim 15 wherein the adeno-associated virus 4 Rep protein has about 95% homology with the amino acid sequence set forth in SEQ ID NO:9
 22. The vector system of claim 15, wherein the adeno-associated virus 4 Rep protein has the amino acid sequence set forth in SEQ ID NO:10.
 23. The vector system of claim 15, wherein the adeno-associated virus 4 Rep protein has about 95% homology with the amino acid sequence set forth in SEQ ID NO:10.
 24. The vector system of claim 15, wherein the adeno-associated virus 4 Rep protein has the amino acid sequence set forth in SEQ ID NO:11.
 25. The vector system of claim 15, wherein the adeno-associated virus 4 Rep protein has about 95% homology with the amino acid sequence set forth in SEQ ID NO:11.
 26. The vector system of claim 3, wherein the first vector further comprises a nucleic acid encoding an AAV5 Rep protein.
 27. The vector system according to claim 4, wherein the first vector further comprises a nucleic acid encoding an AAV2 capsid protein.
 28. The vector system according to claim 4, wherein the first vector further comprises a nucleic acid encoding an AAV3 capsid protein.
 29. The vector system according to claim 4, wherein the first vector further comprises a nucleic acid encoding an AAV4 capsid protein.
 30. The vector system of claim 29, wherein the adeno-associated virus 4 capsid protein has the amino acid sequence set forth in SEQ ID NO:4.
 31. The vector system of claim 29, wherein the adeno-associated virus 4 capsid protein has the amino acid sequence defined by amino acids 438-601 set forth in SEQ ID NO:4.
 32. The vector system of claim 29, wherein the adeno-associated virus 4 capsid protein has about 98% homology to the amino acid sequence set forth in SEQ ID NO:4.
 33. The vector system of claim 29, wherein the adeno-associated virus 4 capsid protein has the amino acid sequence set forth in SEQ ID NO:16.
 34. The vector system of claim 29, wherein the adeno-associated virus 4 capsid protein has about 98% homology to the amino acid sequence set forth in SEQ ID NO:16.
 35. The vector system of claim 29, wherein the adeno-associated virus 4 capsid protein has the amino acid sequence set forth in SEQ ID NO:18.
 36. The vector system of claim 29, wherein the adeno-associated virus 4 capsid protein has about 98% homology to the amino acid sequence set forth in SEQ ID NO:18.
 37. The vector system according to claim 4, wherein the first vector further comprises a nucleic acid encoding an AAV5 capsid protein.
 38. A vector system according to claim 3, wherein the second vector further comprises a promoter between the inverted terminal repeats.
 39. A vector system according to claim 38, wherein the promoter is functionally linked to an exogenous nucleic acid.
 40. The vector system according to claim 2, wherein the system comprises a series of vectors.
 41. A method of making a recombinant particle for delivering an exogenous nucleic acid to a cell, comprising delivering to a cell having helper function the vectors of the vector system of claim
 39. 42. The method of claim 41, wherein the helper function is provided by a helper virus. 